,
Levi Waldron [ctb],
Lucas Schiffer [ctb],
Ludwig Geistlinger [ctb],
Valerie Obenchain [ctb],
Martin Morgan [ctb]| Title: | Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects |
|---|---|
| Description: | This package provides publicly available data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment objects. MultiAssayExperiment integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. It also links assay barcodes with patient identifiers, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment. |
| Authors: | Marcel Ramos [aut, cre] ,
Levi Waldron [ctb],
Lucas Schiffer [ctb],
Ludwig Geistlinger [ctb],
Valerie Obenchain [ctb],
Martin Morgan [ctb] |
| Maintainer: | Marcel Ramos <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.27.0 |
| Built: | 2024-08-29 05:32:53 UTC |
| Source: | https://github.com/waldronlab/curatedTCGAData |
A document describing the TCGA cancer code
> experiments( ACC )
ExperimentList class object of length 10:
[1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 180 columns
[2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 180 columns
[3] ACC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[4] ACC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 42 rows and 90 columns
[5] ACC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[6] ACC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[7] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
[8] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 79 columns
[9] ACC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 46 columns
[10] ACC_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( ACC )
CharacterList of length 10
[["ACC_CNASNP-20160128"]] character(0)
[["ACC_CNVSNP-20160128"]] character(0)
[["ACC_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["ACC_GISTIC_Peaks-20160128"]] chr1:8403012-8925111 ...
[["ACC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["ACC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ACC_Mutation-20160128"]] character(0)
[["ACC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["ACC_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( ACC )
CharacterList of length 10
[["ACC_CNASNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_CNVSNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_AllByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_Peaks-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_ThresholdedByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_miRNASeqGene-20160128"]] TCGA-OR-A5J1-01A-11R-A29W-13 ...
[["ACC_Mutation-20160128"]] TCGA-OR-A5J1-01A-11D-A29I-10 ...
[["ACC_RNASeq2GeneNorm-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RPPAArray-20160128"]] TCGA-OR-A5J2-01A-21-A39K-20 ...
[["ACC_Methylation-20160128"]] TCGA-OR-A5J1-01A-11D-A29J-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 ACC_CNASNP-20160128 2.2 Mb
2 ACC_CNVSNP-20160128 0.6 Mb
3 ACC_GISTIC_AllByGene-20160128 4.9 Mb
4 ACC_GISTIC_Peaks-20160128 0.1 Mb
5 ACC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 ACC_miRNASeqGene-20160128 0.1 Mb
7 ACC_Mutation-20160128 12.6 Mb
8 ACC_RNASeq2GeneNorm-20160128 1.3 Mb
9 ACC_RPPAArray-20160128 0 Mb
10 ACC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
58 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
34.00 34.00 1.51 1.34 3.03
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 35.50 48.50 47.16 60.00 83.00
vital_status:
0 1
58 34
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 399.0 551.5 854.6 1202.2 2405.0 58
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
383.0 917.8 1453.5 1781.6 2339.2 4673.0 34
tumor_tissue_site:
adrenal
92
pathologic_stage:
stage i stage ii stage iii stage iv NA's
9 44 19 18 2
pathology_T_stage:
t1 t2 t3 t4 NA's
9 49 11 21 2
pathology_N_stage:
n0 n1 NA's
80 10 2
gender:
female male
60 32
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1997 2005 2008 2007 2011 2012
radiation_therapy:
no yes NA's
71 18 3
histological_type:
adrenocortical carcinoma- myxoid type
1
adrenocortical carcinoma- oncocytic type
4
adrenocortical carcinoma- usual type
87
residual_tumor:
r0 r1 r2 rx NA's
64 7 12 6 3
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.548 0.500 52.000 61
race:
asian black or african american white
2 1 78
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
8 40 44
Including an additional 806 columns
A document describing the TCGA cancer code
> experiments( BLCA )
ExperimentList class object of length 12:
[1] BLCA_CNASeq-20160128: RaggedExperiment with 35692 rows and 232 columns
[2] BLCA_CNASNP-20160128: RaggedExperiment with 479978 rows and 806 columns
[3] BLCA_CNVSNP-20160128: RaggedExperiment with 104349 rows and 797 columns
[4] BLCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[5] BLCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 71 rows and 408 columns
[6] BLCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[7] BLCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 429 columns
[8] BLCA_Mutation-20160128: RaggedExperiment with 39312 rows and 130 columns
[9] BLCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 427 columns
[10] BLCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 67 columns
[11] BLCA_RPPAArray-20160128: SummarizedExperiment with 208 rows and 344 columns
[12] BLCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 434 columns
> rownames( BLCA )
CharacterList of length 12
[["BLCA_CNASeq-20160128"]] character(0)
[["BLCA_CNASNP-20160128"]] character(0)
[["BLCA_CNVSNP-20160128"]] character(0)
[["BLCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["BLCA_GISTIC_Peaks-20160128"]] chr1:26963410-27155421 ...
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["BLCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["BLCA_Mutation-20160128"]] character(0)
[["BLCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( BLCA )
CharacterList of length 12
[["BLCA_CNASeq-20160128"]] TCGA-BL-A0C8-01A-11D-A10R-02 ...
[["BLCA_CNASNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_CNVSNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_AllByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_Peaks-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_miRNASeqGene-20160128"]] TCGA-2F-A9KO-01A-11R-A38M-13 ...
[["BLCA_Mutation-20160128"]] TCGA-BL-A0C8-01A-11D-A10S-08 ...
[["BLCA_RNASeq2GeneNorm-20160128"]] TCGA-2F-A9KO-01A-11R-A38B-07 ...
[["BLCA_RNASeqGene-20160128"]] TCGA-BL-A0C8-01A-11R-A10U-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BLCA_CNASeq-20160128 1 Mb
2 BLCA_CNASNP-20160128 13.1 Mb
3 BLCA_CNVSNP-20160128 3 Mb
4 BLCA_GISTIC_AllByGene-20160128 4.9 Mb
5 BLCA_GISTIC_Peaks-20160128 0.1 Mb
6 BLCA_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 BLCA_miRNASeqGene-20160128 0.1 Mb
8 BLCA_Mutation-20160128 56.1 Mb
9 BLCA_RNASeq2GeneNorm-20160128 1.3 Mb
10 BLCA_RNASeqGene-20160128 1.3 Mb
11 BLCA_RPPAArray-20160128 0 Mb
12 BLCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
232 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
180.000 180.000 1.125 0.992 1.332
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
34.00 60.00 69.00 68.08 76.00 90.00 1
vital_status:
0 1
230 182
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.0 235.8 410.5 552.8 654.5 3183.0 232
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-64.0 398.2 639.0 1016.7 1458.8 5050.0 182
tumor_tissue_site:
bladder
412
pathologic_stage:
stage i stage ii stage iii stage iv NA's
2 131 141 136 2
pathology_M_stage:
m0 m1 mx NA's
196 11 202 3
gender:
female male
108 304
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1999 2009 2011 2010 2012 2013 18
radiation_therapy:
no yes NA's
366 20 26
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 80.00 90.00 83.09 90.00 100.00 276
histological_type:
muscle invasive urothelial carcinoma (pt2 or above)
409
NA's
3
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.00 30.00 39.04 50.00 730.00 188
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.088 2.000 97.000 115
race:
asian black or african american white
44 23 327
NA's
18
ethnicity:
hispanic or latino not hispanic or latino NA's
9 371 32
Including an additional 1695 columns
A document describing the TCGA cancer code
> experiments( BRCA )
ExperimentList class object of length 14:
[1] BRCA_CNASeq-20160128: RaggedExperiment with 5298 rows and 38 columns
[2] BRCA_CNASNP-20160128: RaggedExperiment with 1132786 rows and 2209 columns
[3] BRCA_CNVSNP-20160128: RaggedExperiment with 284458 rows and 2199 columns
[4] BRCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[5] BRCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 1080 columns
[6] BRCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[7] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
[8] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
[9] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns
[10] BRCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[11] BRCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 878 columns
[12] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[13] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
[14] BRCA_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 885 columns
> rownames( BRCA )
CharacterList of length 14
[["BRCA_CNASeq-20160128"]] character(0)
[["BRCA_CNASNP-20160128"]] character(0)
[["BRCA_CNVSNP-20160128"]] character(0)
[["BRCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["BRCA_GISTIC_Peaks-20160128"]] chr1:12675879-21133098 ...
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["BRCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["BRCA_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["BRCA_Mutation-20160128"]] character(0)
[["BRCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( BRCA )
CharacterList of length 14
[["BRCA_CNASeq-20160128"]] TCGA-A2-A0EU-01A-22D-A060-02 ...
[["BRCA_CNASNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_CNVSNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_AllByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_Peaks-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_miRNASeqGene-20160128"]] TCGA-3C-AAAU-01A-11R-A41G-13 ...
[["BRCA_mRNAArray-20160128"]] TCGA-A1-A0SD-01A-11R-A115-07 ...
[["BRCA_Mutation-20160128"]] TCGA-A1-A0SB-01A-11D-A142-09 ...
[["BRCA_RNASeq2GeneNorm-20160128"]] TCGA-3C-AAAU-01A-11R-A41B-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BRCA_CNASeq-20160128 0.2 Mb
2 BRCA_CNASNP-20160128 30.9 Mb
3 BRCA_CNVSNP-20160128 8.2 Mb
4 BRCA_GISTIC_AllByGene-20160128 5 Mb
5 BRCA_GISTIC_Peaks-20160128 0.2 Mb
6 BRCA_GISTIC_ThresholdedByGene-20160128 5 Mb
7 BRCA_miRNASeqGene-20160128 0.1 Mb
8 BRCA_mRNAArray-20160128 1.2 Mb
9 BRCA_Mutation-20160128 67.4 Mb
10 BRCA_RNASeq2GeneNorm-20160128 1.4 Mb
11 BRCA_RNASeqGene-20160128 1.4 Mb
12 BRCA_RPPAArray-20160128 0.1 Mb
13 BRCA_Methylation_methyl27-20160128 4.9 Mb
14 BRCA_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
947 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
151.00 151.00 3.48 2.83 4.50
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.0 49.0 59.0 58.6 68.0 90.0 16
vital_status:
0 1 NA's
945 152 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
116.0 700.5 1272.0 1644.7 2367.0 7455.0 947
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-7 440 761 1183 1572 8605 153
tumor_tissue_site:
breast NA's
1097 1
pathology_M_stage:
cm0 (i+) m0 m1 mx NA's
6 906 22 163 1
gender:
female male NA's
1085 12 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1988 2007 2009 2008 2010 2013 3
days_to_last_known_alive:
735 2576 NA's
1 1 1096
radiation_therapy:
no yes NA's
446 556 96
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.363 2.000 35.000 169
race:
american indian or alaska native asian
1 61
black or african american white
183 757
NA's
96
ethnicity:
hispanic or latino not hispanic or latino NA's
39 884 175
Including an additional 2667 columns
A document describing the TCGA cancer code
> experiments( CESC )
ExperimentList class object of length 11:
[1] CESC_CNASeq-20160128: RaggedExperiment with 7834 rows and 100 columns
[2] CESC_CNASNP-20160128: RaggedExperiment with 267855 rows and 586 columns
[3] CESC_CNVSNP-20160128: RaggedExperiment with 59450 rows and 586 columns
[4] CESC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[5] CESC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 60 rows and 295 columns
[6] CESC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[7] CESC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 312 columns
[8] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
[9] CESC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 309 columns
[10] CESC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 173 columns
[11] CESC_Methylation-20160128: SummarizedExperiment with 485577 rows and 312 columns
> rownames( CESC )
CharacterList of length 11
[["CESC_CNASeq-20160128"]] character(0)
[["CESC_CNASNP-20160128"]] character(0)
[["CESC_CNVSNP-20160128"]] character(0)
[["CESC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["CESC_GISTIC_Peaks-20160128"]] chr1:1-28840301 ... chr22:48668582-51304566
[["CESC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["CESC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CESC_Mutation-20160128"]] character(0)
[["CESC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["CESC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( CESC )
CharacterList of length 11
[["CESC_CNASeq-20160128"]] TCGA-C5-A1BQ-01C-11D-A20X-26 ...
[["CESC_CNASNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_CNVSNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_AllByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_Peaks-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_miRNASeqGene-20160128"]] TCGA-2W-A8YY-01A-11R-A37P-13 ...
[["CESC_Mutation-20160128"]] TCGA-BI-A0VR-01A-11D-A10S-08 ...
[["CESC_RNASeq2GeneNorm-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
[["CESC_RPPAArray-20160128"]] TCGA-2W-A8YY-01A-21-A40H-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 CESC_CNASeq-20160128 0.3 Mb
2 CESC_CNASNP-20160128 7.3 Mb
3 CESC_CNVSNP-20160128 1.8 Mb
4 CESC_GISTIC_AllByGene-20160128 4.9 Mb
5 CESC_GISTIC_Peaks-20160128 0.1 Mb
6 CESC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 CESC_miRNASeqGene-20160128 0.1 Mb
8 CESC_Mutation-20160128 32.9 Mb
9 CESC_RNASeq2GeneNorm-20160128 1.3 Mb
10 CESC_RPPAArray-20160128 0 Mb
11 CESC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
235 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
72.00 72.00 1.70 1.39 2.29
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 38.0 46.0 48.2 56.0 88.0 2
vital_status:
0 1
235 72
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 349.5 620.0 881.3 1069.5 4086.0 235
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 374 688 1071 1362 6408 72
tumor_tissue_site:
cervical
307
pathology_N_stage:
n0 n1 nx NA's
135 60 67 45
pathology_M_stage:
m0 m1 mx NA's
116 10 131 50
gender:
female
307
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
radiation_therapy:
no yes NA's
55 129 123
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
ethnicity:
hispanic or latino not hispanic or latino NA's
24 171 112
weight_kg_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.25 70.50 73.04 83.75 210.00 29
tumor_status:
tumor free with tumor NA's
201 80 26
tobacco_smoking_year_stopped:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1995 2003 2000 2010 2013 264
tobacco_smoking_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
tobacco_smoking_history:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 1.000 1.829 2.000 5.000 44
agebegansmokinginyears:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.00 16.00 18.00 21.14 24.00 44.00 222
radiation_therapy_status:
completed as planned treatment not completed NA's
29 3 275
pregnancies_count_total:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 2.00 3.00 3.61 5.00 15.00 40
pregnancies_count_stillbirth:
0 1 3 NA's
106 5 1 195
pregnancy_spontaneous_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.5442 1.0000 6.0000 160
pregnancies_count_live_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.250 2.000 2.844 4.000 11.000 45
pregnancy_therapeutic_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.8525 1.0000 13.0000 185
pregnancies_count_ectopic:
0 1 2 NA's
104 11 1 191
lymph_node_location:
lymph_node_location_positive_pathology_name|lymph_node_location_positive_pathology_text
307
menopause_status:
indeterminate (neither pre or postmenopausal)
3
peri (6-12 months since last menstrual period)
25
post (prior bilateral ovariectomy or >12 mo since lmp with no prior hysterectomy)
84
pre (<6 months since lmp and no prior bilateral ovariectomy and not on estrogen replacement)
125
NA's
70
lymphovascular_involvement:
absent present NA's
72 80 155
lymph_nodes_examined_he_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
lymph_nodes_examined:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.00 13.00 21.00 22.28 29.00 63.00 127
keratinization_squamous_cell:
keratinizing squamous cell carcinoma
55
non-keratinizing squamous cell carcinoma
120
NA's
132
initial_pathologic_dx_year:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
hysterectomy_type:
hysterectomy_performed_type|hysterectomy_performed_text
307
history_hormonal_contraceptives_use:
current user former user never used NA's
15 54 90 148
height_cm_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
132 157 160 161 165 183 43
corpus_involvement:
absent present NA's
99 19 189
chemo_concurrent_type:
carboplatin cisplatin other NA's
7 104 2 194
cervix_suv_results:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 8.70 12.00 13.22 16.92 28.80 290
cause_of_death:
cardiopulmonary arrest lung cancer renal failure
1 1 1
NA's
304
age_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
20.00 38.00 46.00 48.27 56.50 88.00
Including an additional 1330 columns
A document describing the TCGA cancer code
> experiments( CHOL )
ExperimentList class object of length 10:
[1] CHOL_CNASNP-20160128: RaggedExperiment with 39698 rows and 85 columns
[2] CHOL_CNVSNP-20160128: RaggedExperiment with 7570 rows and 85 columns
[3] CHOL_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[4] CHOL_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 19 rows and 36 columns
[5] CHOL_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[6] CHOL_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 45 columns
[7] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns
[8] CHOL_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 45 columns
[9] CHOL_RPPAArray-20160128: SummarizedExperiment with 192 rows and 30 columns
[10] CHOL_Methylation-20160128: SummarizedExperiment with 485577 rows and 45 columns
> rownames( CHOL )
CharacterList of length 10
[["CHOL_CNASNP-20160128"]] character(0)
[["CHOL_CNVSNP-20160128"]] character(0)
[["CHOL_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["CHOL_GISTIC_Peaks-20160128"]] chr1:7829287-29140747 ... chr16:1-90354753
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["CHOL_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CHOL_Mutation-20160128"]] character(0)
[["CHOL_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["CHOL_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CHOL_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( CHOL )
CharacterList of length 10
[["CHOL_CNASNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_CNVSNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_AllByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_Peaks-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_miRNASeqGene-20160128"]] TCGA-3X-AAV9-01A-72R-A41D-13 ...
[["CHOL_Mutation-20160128"]] TCGA-3X-AAV9-01A-72D-A417-09 ...
[["CHOL_RNASeq2GeneNorm-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ...
[["CHOL_RPPAArray-20160128"]] TCGA-3X-AAV9-01A-81-A45N-20 ...
[["CHOL_Methylation-20160128"]] TCGA-3X-AAV9-01A-72D-A418-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 CHOL_CNASNP-20160128 1.1 Mb
2 CHOL_CNVSNP-20160128 0.2 Mb
3 CHOL_GISTIC_AllByGene-20160128 4.9 Mb
4 CHOL_GISTIC_Peaks-20160128 0 Mb
5 CHOL_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 CHOL_miRNASeqGene-20160128 0.1 Mb
7 CHOL_Mutation-20160128 4.6 Mb
8 CHOL_RNASeq2GeneNorm-20160128 1.3 Mb
9 CHOL_RPPAArray-20160128 0 Mb
10 CHOL_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
18 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
18.000 18.000 1.370 0.742 2.532
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 56.50 66.50 63.03 72.00 82.00
vital_status:
0 1
18 18
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
21.0 195.2 500.0 592.9 731.0 1939.0 18
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.0 539.8 942.5 936.6 1394.0 1976.0 18
tumor_tissue_site:
bile duct
36
pathology_T_stage:
t1 t2 t2a t2b t3
19 6 2 4 5
pathology_N_stage:
n0 n1 nx
26 5 5
pathology_M_stage:
m0 m1 mx
28 5 3
gender:
female male
20 16
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2005 2010 2011 2010 2012 2013
radiation_therapy:
no NA's
35 1
histological_type:
cholangiocarcinoma; distal cholangiocarcinoma; hilar/perihilar
2 4
cholangiocarcinoma; intrahepatic
30
residual_tumor:
r0 r1 rx
28 5 3
race:
asian black or african american white
3 2 31
ethnicity:
hispanic or latino not hispanic or latino NA's
2 33 1
Including an additional 622 columns
A document describing the TCGA cancer code
> experiments( COAD )
ExperimentList class object of length 14:
[1] COAD_CNASeq-20160128: RaggedExperiment with 40530 rows and 136 columns
[2] COAD_CNASNP-20160128: RaggedExperiment with 459490 rows and 914 columns
[3] COAD_CNVSNP-20160128: RaggedExperiment with 90534 rows and 914 columns
[4] COAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[5] COAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 66 rows and 449 columns
[6] COAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[7] COAD_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 221 columns
[8] COAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 172 columns
[9] COAD_Mutation-20160128: RaggedExperiment with 62530 rows and 154 columns
[10] COAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 191 columns
[11] COAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 10 columns
[12] COAD_RPPAArray-20160128: SummarizedExperiment with 208 rows and 360 columns
[13] COAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 202 columns
[14] COAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 333 columns
> rownames( COAD )
CharacterList of length 14
[["COAD_CNASeq-20160128"]] character(0)
[["COAD_CNASNP-20160128"]] character(0)
[["COAD_CNVSNP-20160128"]] character(0)
[["COAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["COAD_GISTIC_Peaks-20160128"]] chr1:26527443-27650365 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["COAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["COAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["COAD_Mutation-20160128"]] character(0)
[["COAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( COAD )
CharacterList of length 14
[["COAD_CNASeq-20160128"]] TCGA-A6-2671-01A-01D-1405-02 ...
[["COAD_CNASNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_CNVSNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_AllByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_Peaks-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_miRNASeqGene-20160128"]] TCGA-A6-2675-01A-02T-1722-13 ...
[["COAD_mRNAArray-20160128"]] TCGA-A6-2671-11A-01R-1758-07 ...
[["COAD_Mutation-20160128"]] TCGA-A6-2672-01A-01W-0833-10 ...
[["COAD_RNASeq2GeneNorm-20160128"]] TCGA-A6-2671-01A-01R-1410-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 COAD_CNASeq-20160128 1.1 Mb
2 COAD_CNASNP-20160128 12.5 Mb
3 COAD_CNVSNP-20160128 2.7 Mb
4 COAD_GISTIC_AllByGene-20160128 4.9 Mb
5 COAD_GISTIC_Peaks-20160128 0.1 Mb
6 COAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 COAD_miRNASeqGene-20160128 0.1 Mb
8 COAD_mRNAArray-20160128 1.1 Mb
9 COAD_Mutation-20160128 23.6 Mb
10 COAD_RNASeq2GeneNorm-20160128 1.3 Mb
11 COAD_RNASeqGene-20160128 1.3 Mb
12 COAD_RPPAArray-20160128 0 Mb
13 COAD_Methylation_methyl27-20160128 4.9 Mb
14 COAD_Methylation_methyl450-20160128 75 Mb
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.00 68.00 66.95 77.00 90.00 2
tumor_tissue_site:
colon NA's
456 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2007 2009 2008 2010 2013
radiation_therapy:
no yes NA's
378 9 70
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.058 2.000 50.000 25
race:
american indian or alaska native asian
1 11
black or african american white
59 213
NA's
173
ethnicity:
hispanic or latino not hispanic or latino NA's
4 270 183
Including an additional 2604 columns
A document describing the TCGA cancer code
> experiments( DLBC )
ExperimentList class object of length 10:
[1] DLBC_CNASNP-20160128: RaggedExperiment with 44725 rows and 94 columns
[2] DLBC_CNVSNP-20160128: RaggedExperiment with 9343 rows and 94 columns
[3] DLBC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[4] DLBC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 39 rows and 48 columns
[5] DLBC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[6] DLBC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 47 columns
[7] DLBC_Mutation-20160128: RaggedExperiment with 16918 rows and 48 columns
[8] DLBC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 48 columns
[9] DLBC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 33 columns
[10] DLBC_Methylation-20160128: SummarizedExperiment with 485577 rows and 48 columns
> rownames( DLBC )
CharacterList of length 10
[["DLBC_CNASNP-20160128"]] character(0)
[["DLBC_CNVSNP-20160128"]] character(0)
[["DLBC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["DLBC_GISTIC_Peaks-20160128"]] chr1:1-48649489 ... chr22:41635693-51304566
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["DLBC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["DLBC_Mutation-20160128"]] character(0)
[["DLBC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["DLBC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["DLBC_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( DLBC )
CharacterList of length 10
[["DLBC_CNASNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_CNVSNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_AllByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_Peaks-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_miRNASeqGene-20160128"]] TCGA-FA-8693-01A-11R-2401-13 ...
[["DLBC_Mutation-20160128"]] TCGA-FA-8693-01A-11D-2397-10 ...
[["DLBC_RNASeq2GeneNorm-20160128"]] TCGA-FA-8693-01A-11R-2404-07 ...
[["DLBC_RPPAArray-20160128"]] TCGA-FA-8693-01A-21-A45K-20 ...
[["DLBC_Methylation-20160128"]] TCGA-FA-8693-01A-11D-2399-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 DLBC_CNASNP-20160128 1.2 Mb
2 DLBC_CNVSNP-20160128 0.3 Mb
3 DLBC_GISTIC_AllByGene-20160128 4.9 Mb
4 DLBC_GISTIC_Peaks-20160128 0 Mb
5 DLBC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 DLBC_miRNASeqGene-20160128 0.1 Mb
7 DLBC_Mutation-20160128 12.6 Mb
8 DLBC_RNASeq2GeneNorm-20160128 1.3 Mb
9 DLBC_RPPAArray-20160128 0 Mb
10 DLBC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
39 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.000 9.000 1.630 0.858 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
23.00 46.00 57.50 56.27 67.00 82.00
vital_status:
0 1
39 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
58 313 595 1505 1252 6425 39
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 616 946 1328 1581 5980 9
gender:
female male
26 22
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1987 2009 2011 2009 2012 2013
radiation_therapy:
no yes NA's
40 7 1
histological_type:
diffuse large b-cell lymphoma (dlbcl) nos (any anatomic site nodal or extranodal)
41
primary dlbcl of the cns
3
primary mediastinal (thymic) dlbcl
4
race:
asian black or african american white
18 1 29
ethnicity:
hispanic or latino not hispanic or latino
12 36
Including an additional 607 columns
A document describing the TCGA cancer code
> experiments( ESCA )
ExperimentList class object of length 12:
[1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns
[2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns
[3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns
[4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns
[6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[7] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns
[8] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
[9] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 196 columns
[10] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns
[11] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns
[12] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns
> rownames( ESCA )
CharacterList of length 12
[["ESCA_CNASeq-20160128"]] character(0)
[["ESCA_CNASNP-20160128"]] character(0)
[["ESCA_CNVSNP-20160128"]] character(0)
[["ESCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["ESCA_GISTIC_Peaks-20160128"]] chr1:23960869-31653987 ... chr22:1-18218209
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["ESCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ESCA_Mutation-20160128"]] character(0)
[["ESCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["ESCA_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
...
<2 more elements>
> colnames( ESCA )
CharacterList of length 12
[["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ...
[["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_miRNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37J-13 ...
[["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ...
[["ESCA_RNASeq2GeneNorm-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 ESCA_CNASeq-20160128 0.5 Mb
2 ESCA_CNASNP-20160128 5.5 Mb
3 ESCA_CNVSNP-20160128 1.7 Mb
4 ESCA_GISTIC_AllByGene-20160128 4.9 Mb
5 ESCA_GISTIC_Peaks-20160128 0.1 Mb
6 ESCA_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 ESCA_miRNASeqGene-20160128 0.1 Mb
8 ESCA_Mutation-20160128 45 Mb
9 ESCA_RNASeq2GeneNorm-20160128 1.3 Mb
10 ESCA_RNASeqGene-20160128 1.7 Mb
11 ESCA_RPPAArray-20160128 0 Mb
12 ESCA_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
108 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
77.000 77.000 0.962 0.677 1.353
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 54.00 61.00 62.46 72.00 90.00
vital_status:
0 1
108 77
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 180.0 351.0 495.2 650.0 2532.0 108
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 336.5 402.5 570.1 696.8 3714.0 77
tumor_tissue_site:
esophagus
185
pathology_M_stage:
m0 m1 m1a mx NA's
136 4 5 18 22
gender:
female male
27 158
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1998 2007 2011 2009 2012 2013 7
radiation_therapy:
no yes NA's
124 43 18
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 60.00 80.00 73.82 90.00 100.00 117
histological_type:
esophagus adenocarcinoma, nos esophagus squamous cell carcinoma
89 96
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 17.62 30.00 34.48 47.25 102.00 87
residual_tumor:
r0 r1 r2 rx NA's
137 13 2 7 26
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.526 4.000 21.000 50
race:
asian black or african american white
46 5 114
NA's
20
ethnicity:
hispanic or latino not hispanic or latino NA's
6 88 91
Including an additional 940 columns
A document describing the TCGA cancer code
> experiments( GBM )
ExperimentList class object of length 18:
[1] GBM_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 81512 rows and 438 columns
[2] GBM_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 57975 rows and 338 columns
[3] GBM_CNASNP-20160128: RaggedExperiment with 602338 rows and 1104 columns
[4] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
[5] GBM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[6] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
[7] GBM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[8] GBM_miRNAArray-20160128: SummarizedExperiment with 534 rows and 565 columns
[9] GBM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 0 columns
[10] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns
[11] GBM_mRNAArray_TX_g4502a_1-20160128: SummarizedExperiment with 17814 rows and 401 columns
[12] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 101 columns
[13] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns
[14] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns
[15] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns
[16] GBM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 244 columns
[17] GBM_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 285 columns
[18] GBM_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 154 columns
> rownames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["GBM_CNASNP-20160128"]] character(0)
[["GBM_CNVSNP-20160128"]] character(0)
[["GBM_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["GBM_GISTIC_Peaks-20160128"]] chr1:3394251-6475685 ...
[["GBM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["GBM_miRNAArray-20160128"]] ebv-miR-BART1-3p ... kshv-miR-K12-9*
[["GBM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["GBM_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
...
<8 more elements>
> colnames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] TCGA-02-0001-01C-01D-0185-02 ...
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-02-2466-01A-01D-0787-02 ...
[["GBM_CNASNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_CNVSNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_AllByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_Peaks-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_ThresholdedByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_miRNAArray-20160128"]] TCGA-02-0001-01C-01T-0179-07 ...
[["GBM_miRNASeqGene-20160128"]] character(0)
[["GBM_mRNAArray_huex-20160128"]] TCGA-02-0001-01C-01R-0178-03 ...
...
<8 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 GBM_CNACGH_CGH_hg_244a-20160128 2.3 Mb
2 GBM_CNACGH_CGH_hg_415k_g4124a-20160128 1.7 Mb
3 GBM_CNASNP-20160128 16.4 Mb
4 GBM_CNVSNP-20160128 4.2 Mb
5 GBM_GISTIC_AllByGene-20160128 4.9 Mb
6 GBM_GISTIC_Peaks-20160128 0.1 Mb
7 GBM_GISTIC_ThresholdedByGene-20160128 4.9 Mb
8 GBM_miRNAArray-20160128 0.1 Mb
9 GBM_miRNASeqGene-20160128 0.1 Mb
10 GBM_mRNAArray_huex-20160128 1.2 Mb
11 GBM_mRNAArray_TX_g4502a_1-20160128 1.1 Mb
12 GBM_mRNAArray_TX_g4502a-20160128 1.1 Mb
13 GBM_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb
14 GBM_Mutation-20160128 31 Mb
15 GBM_RNASeq2GeneNorm-20160128 1.3 Mb
16 GBM_RPPAArray-20160128 0 Mb
17 GBM_Methylation_methyl27-20160128 4.9 Mb
18 GBM_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
109 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
490.000 490.000 1.047 0.981 1.156
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.00 50.00 59.00 57.82 68.00 89.00 4
vital_status:
0 1 NA's
104 491 4
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 170.5 382.0 504.5 609.2 3881.0 109
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 156.2 261.0 479.4 628.0 2818.0 497
tumor_tissue_site:
brain NA's
595 4
gender:
female male NA's
230 365 4
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1989 2002 2006 2005 2009 2013 4
radiation_therapy:
no yes NA's
78 489 32
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 70.00 80.00 77.04 80.00 100.00 157
histological_type:
glioblastoma multiforme (gbm) treated primary gbm
31 20
untreated primary (de novo) gbm NA's
544 4
race:
asian black or african american white
13 51 506
NA's
29
ethnicity:
hispanic or latino not hispanic or latino NA's
13 489 97
Including an additional 4368 columns
A document describing the TCGA cancer code
> experiments( HNSC )
ExperimentList class object of length 12:
[1] HNSC_CNASeq-20160128: RaggedExperiment with 32905 rows and 225 columns
[2] HNSC_CNASNP-20160128: RaggedExperiment with 499142 rows and 1090 columns
[3] HNSC_CNVSNP-20160128: RaggedExperiment with 110289 rows and 1089 columns
[4] HNSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[5] HNSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 72 rows and 522 columns
[6] HNSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[7] HNSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
[8] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
[9] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 566 columns
[10] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
[11] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
[12] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns
> rownames( HNSC )
CharacterList of length 12
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["HNSC_GISTIC_Peaks-20160128"]] chr1:1-27864255 ... chr21:41298805-43485528
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["HNSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( HNSC )
CharacterList of length 12
[["HNSC_CNASeq-20160128"]] TCGA-BA-4074-01A-01D-1431-02 ...
[["HNSC_CNASNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_CNVSNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_AllByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_Peaks-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_miRNASeqGene-20160128"]] TCGA-4P-AA8J-01A-11R-A39B-13 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2GeneNorm-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeqGene-20160128"]] TCGA-BA-4074-01A-01R-1436-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 HNSC_CNASeq-20160128 1 Mb
2 HNSC_CNASNP-20160128 13.6 Mb
3 HNSC_CNVSNP-20160128 3.3 Mb
4 HNSC_GISTIC_AllByGene-20160128 4.9 Mb
5 HNSC_GISTIC_Peaks-20160128 0.1 Mb
6 HNSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 HNSC_miRNASeqGene-20160128 0.1 Mb
8 HNSC_Mutation-20160128 68.9 Mb
9 HNSC_RNASeq2GeneNorm-20160128 1.3 Mb
10 HNSC_RNASeqGene-20160128 1.3 Mb
11 HNSC_RPPAArray-20160128 0 Mb
12 HNSC_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
305 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
223.00 223.00 1.18 1.06 1.35
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.00 53.00 61.00 60.91 69.00 89.00 1
vital_status:
0 1
304 224
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 260.0 430.0 740.0 814.5 6417.0 305
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.0 529.5 851.0 1042.9 1404.0 5480.0 225
tumor_tissue_site:
head and neck
528
pathology_M_stage:
m0 m1 mx NA's
191 1 65 271
gender:
female male
142 386
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2007 2010 2008 2011 2013 1
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
98.0 483.0 848.5 1226.9 1647.5 3930.0 506
radiation_therapy:
no yes NA's
163 303 62
histological_type:
head & neck squamous cell carcinoma
517
head & neck squamous cell carcinoma basaloid type
10
head & neck squamous cell carcinoma, spindle cell variant
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.01685 25.00000 40.00000 45.75496 60.00000 300.00000 230
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1936 1959 1968 1967 1975 2001 246
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.186 3.000 44.000 115
race:
american indian or alaska native asian
2 11
black or african american white
48 452
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
26 465 37
Including an additional 1426 columns
A document describing the TCGA cancer code
> experiments( KICH )
ExperimentList class object of length 10:
[1] KICH_CNASNP-20160128: RaggedExperiment with 57729 rows and 132 columns
[2] KICH_CNVSNP-20160128: RaggedExperiment with 10164 rows and 132 columns
[3] KICH_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[4] KICH_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 2 rows and 66 columns
[5] KICH_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[6] KICH_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 91 columns
[7] KICH_Mutation-20160128: RaggedExperiment with 7559 rows and 66 columns
[8] KICH_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 91 columns
[9] KICH_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[10] KICH_Methylation-20160128: SummarizedExperiment with 485577 rows and 66 columns
> rownames( KICH )
CharacterList of length 10
[["KICH_CNASNP-20160128"]] character(0)
[["KICH_CNVSNP-20160128"]] character(0)
[["KICH_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["KICH_GISTIC_Peaks-20160128"]] chr8:116272008-117149163 chr15:1-66482794
[["KICH_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["KICH_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KICH_Mutation-20160128"]] character(0)
[["KICH_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["KICH_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["KICH_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( KICH )
CharacterList of length 10
[["KICH_CNASNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_CNVSNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_AllByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_Peaks-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_ThresholdedByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_miRNASeqGene-20160128"]] TCGA-KL-8323-01A-21R-2314-13 ...
[["KICH_Mutation-20160128"]] TCGA-KL-8323-01A-21D-2310-10 ...
[["KICH_RNASeq2GeneNorm-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ...
[["KICH_RPPAArray-20160128"]] TCGA-KL-8324-01A-21-A421-20 ...
[["KICH_Methylation-20160128"]] TCGA-KL-8323-01A-21D-2312-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 KICH_CNASNP-20160128 1.6 Mb
2 KICH_CNVSNP-20160128 0.3 Mb
3 KICH_GISTIC_AllByGene-20160128 4.9 Mb
4 KICH_GISTIC_Peaks-20160128 0 Mb
5 KICH_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 KICH_miRNASeqGene-20160128 0.1 Mb
7 KICH_Mutation-20160128 2.6 Mb
8 KICH_RNASeq2GeneNorm-20160128 1.3 Mb
9 KICH_RPPAArray-20160128 0 Mb
10 KICH_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.00 9.00 2.34 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
17.00 42.00 50.00 51.52 61.75 86.00
vital_status:
0 1
56 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
325 725 855 1001 1158 2172 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 1366 2713 2320 3138 4676 10
tumor_tissue_site:
kidney
66
pathologic_stage:
stage i stage ii stage iii stage iv
21 25 14 6
pathology_N_stage:
n0 n1 n2 nx
40 3 2 21
pathology_M_stage:
m0 m1 mx NA's
34 2 9 21
gender:
female male
27 39
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2000 2004 2005 2005 2007 2011
radiation_therapy:
no
66
karnofsky_performance_score:
90 100 NA's
3 10 53
histological_type:
kidney chromophobe
66
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 8.00 24.00 25.09 31.00 75.00 55
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1964 1974 1974 1984 1997 58
race:
asian black or african american white
2 4 58
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
4 32 30
Including an additional 718 columns
A document describing the TCGA cancer code
> experiments( KIRC )
ExperimentList class object of length 13:
[1] KIRC_CNASNP-20160128: RaggedExperiment with 488691 rows and 1059 columns
[2] KIRC_CNVSNP-20160128: RaggedExperiment with 85036 rows and 1059 columns
[3] KIRC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[4] KIRC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 26 rows and 528 columns
[5] KIRC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[6] KIRC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[7] KIRC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[8] KIRC_Mutation-20160128: RaggedExperiment with 26369 rows and 437 columns
[9] KIRC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 606 columns
[10] KIRC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 537 columns
[11] KIRC_RPPAArray-20160128: SummarizedExperiment with 217 rows and 478 columns
[12] KIRC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 418 columns
[13] KIRC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 480 columns
> rownames( KIRC )
CharacterList of length 13
[["KIRC_CNASNP-20160128"]] character(0)
[["KIRC_CNVSNP-20160128"]] character(0)
[["KIRC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["KIRC_GISTIC_Peaks-20160128"]] chr1:1-31345223 ... chr14:56181301-107349540
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["KIRC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KIRC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRC_Mutation-20160128"]] character(0)
[["KIRC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["KIRC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( KIRC )
CharacterList of length 13
[["KIRC_CNASNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_CNVSNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_AllByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_Peaks-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_miRNASeqGene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37P-13 ...
[["KIRC_mRNAArray-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ...
[["KIRC_Mutation-20160128"]] TCGA-A3-3308-01A-01D-0966-08 ...
[["KIRC_RNASeq2GeneNorm-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
[["KIRC_RNASeqGene-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRC_CNASNP-20160128 13.4 Mb
2 KIRC_CNVSNP-20160128 2.6 Mb
3 KIRC_GISTIC_AllByGene-20160128 4.9 Mb
4 KIRC_GISTIC_Peaks-20160128 0.1 Mb
5 KIRC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 KIRC_miRNASeqGene-20160128 0.1 Mb
7 KIRC_mRNAArray-20160128 1.1 Mb
8 KIRC_Mutation-20160128 8.2 Mb
9 KIRC_RNASeq2GeneNorm-20160128 1.3 Mb
10 KIRC_RNASeqGene-20160128 1.3 Mb
11 KIRC_RPPAArray-20160128 0.1 Mb
12 KIRC_Methylation_methyl27-20160128 4.9 Mb
13 KIRC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
360 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
177.00 177.00 2.24 1.77 2.61
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 52.00 61.00 60.57 70.00 90.00 1
vital_status:
0 1
360 177
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 333.0 819.0 961.2 1432.0 3615.0 360
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 710.5 1454.5 1536.9 2172.0 4537.0 177
tumor_tissue_site:
kidney
537
pathologic_stage:
stage i stage ii stage iii stage iv NA's
269 57 125 84 2
pathology_N_stage:
n0 n1 nx
240 17 280
pathology_M_stage:
m0 m1 mx NA's
426 79 30 2
gender:
female male
191 346
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2004 2006 2006 2007 2013
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 191 1172 1117 1887 2799 510
radiation_therapy:
no yes NA's
142 2 393
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 85.56 100.00 100.00 483
histological_type:
kidney clear cell renal carcinoma
537
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7.00 14.00 30.00 28.33 40.00 65.00 516
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1946 1966 1978 1979 1996 2001 525
race:
asian black or african american white
8 56 466
NA's
7
ethnicity:
hispanic or latino not hispanic or latino NA's
26 359 152
Including an additional 2250 columns
A document describing the TCGA cancer code
> experiments( KIRP )
ExperimentList class object of length 13:
[1] KIRP_CNASNP-20160128: RaggedExperiment with 300681 rows and 593 columns
[2] KIRP_CNVSNP-20160128: RaggedExperiment with 46914 rows and 590 columns
[3] KIRP_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[4] KIRP_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 28 rows and 288 columns
[5] KIRP_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[6] KIRP_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[7] KIRP_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 16 columns
[8] KIRP_Mutation-20160128: RaggedExperiment with 15585 rows and 161 columns
[9] KIRP_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 323 columns
[10] KIRP_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 14 columns
[11] KIRP_RPPAArray-20160128: SummarizedExperiment with 195 rows and 216 columns
[12] KIRP_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 21 columns
[13] KIRP_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 321 columns
> rownames( KIRP )
CharacterList of length 13
[["KIRP_CNASNP-20160128"]] character(0)
[["KIRP_CNVSNP-20160128"]] character(0)
[["KIRP_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["KIRP_GISTIC_Peaks-20160128"]] chr1:1-29472434 ... chr22:29969457-30128393
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["KIRP_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KIRP_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRP_Mutation-20160128"]] character(0)
[["KIRP_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["KIRP_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( KIRP )
CharacterList of length 13
[["KIRP_CNASNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_CNVSNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_AllByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_Peaks-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_miRNASeqGene-20160128"]] TCGA-2K-A9WE-01A-11R-A38N-13 ...
[["KIRP_mRNAArray-20160128"]] TCGA-AL-3466-01A-01R-1193-07 ...
[["KIRP_Mutation-20160128"]] TCGA-A4-7286-01A-11D-2136-08 ...
[["KIRP_RNASeq2GeneNorm-20160128"]] TCGA-2K-A9WE-01A-11R-A38C-07 ...
[["KIRP_RNASeqGene-20160128"]] TCGA-AL-3466-01A-02R-1351-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRP_CNASNP-20160128 8.2 Mb
2 KIRP_CNVSNP-20160128 1.4 Mb
3 KIRP_GISTIC_AllByGene-20160128 4.9 Mb
4 KIRP_GISTIC_Peaks-20160128 0.1 Mb
5 KIRP_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 KIRP_miRNASeqGene-20160128 0.1 Mb
7 KIRP_mRNAArray-20160128 1.1 Mb
8 KIRP_Mutation-20160128 10.6 Mb
9 KIRP_RNASeq2GeneNorm-20160128 1.3 Mb
10 KIRP_RNASeqGene-20160128 1.3 Mb
11 KIRP_RPPAArray-20160128 0 Mb
12 KIRP_Methylation_methyl27-20160128 4.9 Mb
13 KIRP_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
44.00 44.00 1.76 1.35 3.60
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 53.25 61.50 61.52 71.00 88.00 5
vital_status:
0 1
247 44
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
122.0 341.2 641.0 989.8 1498.5 2941.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 438.2 774.5 1070.2 1513.0 5925.0 45
tumor_tissue_site:
kidney
291
pathologic_stage:
stage i stage ii stage iii stage iv NA's
173 21 52 15 30
pathology_N_stage:
n0 n1 n2 nx NA's
50 24 4 212 1
pathology_M_stage:
m0 m1 mx NA's
95 9 172 15
gender:
female male
77 214
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2008 2011 2010 2012 2013 25
days_to_last_known_alive:
34 NA's
1 290
radiation_therapy:
no yes NA's
209 1 81
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 87.66 100.00 100.00 214
histological_type:
kidney papillary renal cell carcinoma
291
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.00 15.00 24.50 31.73 41.25 185.00 215
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1941 1961 1970 1972 1984 2010 235
race:
american indian or alaska native asian
2 6
black or african american white
61 207
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
12 243 36
Including an additional 1686 columns
A document describing the TCGA cancer code
> experiments( LAML )
ExperimentList class object of length 10:
[1] LAML_CNASNP-20160128: RaggedExperiment with 874897 rows and 392 columns
[2] LAML_CNVSNP-20160128: RaggedExperiment with 28324 rows and 380 columns
[3] LAML_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[4] LAML_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 191 columns
[5] LAML_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[6] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns
[7] LAML_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 173 columns
[8] LAML_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 179 columns
[9] LAML_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 194 columns
[10] LAML_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 194 columns
> rownames( LAML )
CharacterList of length 10
[["LAML_CNASNP-20160128"]] character(0)
[["LAML_CNVSNP-20160128"]] character(0)
[["LAML_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LAML_GISTIC_Peaks-20160128"]] chr1:47516423-47533836 ...
[["LAML_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LAML_Mutation-20160128"]] character(0)
[["LAML_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeqGene-20160128"]] AADACL3 AADACL4 ABCA4 ... XGPY2 XKRY2 ZFY
[["LAML_Methylation_methyl27-20160128"]] cg00000292 cg00002426 ... cg27665659
[["LAML_Methylation_methyl450-20160128"]] cg00000029 cg00000108 ... rs9839873
> colnames( LAML )
CharacterList of length 10
[["LAML_CNASNP-20160128"]] TCGA-AB-2802-03A-01D-0756-21 ...
[["LAML_CNVSNP-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_AllByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_Peaks-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_ThresholdedByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_Mutation-20160128"]] TCGA-AB-2802-03B-01W-0728-08 ...
[["LAML_RNASeq2GeneNorm-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeqGene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_Methylation_methyl27-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ...
[["LAML_Methylation_methyl450-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 LAML_CNASNP-20160128 23.5 Mb
2 LAML_CNVSNP-20160128 0.9 Mb
3 LAML_GISTIC_AllByGene-20160128 4.9 Mb
4 LAML_GISTIC_Peaks-20160128 0 Mb
5 LAML_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 LAML_Mutation-20160128 2.8 Mb
7 LAML_RNASeq2GeneNorm-20160128 1.3 Mb
8 LAML_RNASeqGene-20160128 1.3 Mb
9 LAML_Methylation_methyl27-20160128 4.9 Mb
10 LAML_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
80 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
120.000 120.000 0.748 0.586 0.918
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
18.00 44.75 57.00 55.02 67.00 88.00
vital_status:
0 1
67 133
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 91.5 273.0 355.7 489.0 1706.0 80
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 296.2 699.0 913.5 1506.8 2861.0 132
tumor_tissue_site:
bone marrow NA's
199 1
gender:
female male
91 109
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2001 2004 2006 2006 2008 2010
race:
asian black or african american white
2 15 181
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
3 194 3
Including an additional 478 columns
A document describing the TCGA cancer code
> experiments( LGG )
ExperimentList class object of length 12:
[1] LGG_CNASeq-20160128: RaggedExperiment with 6360 rows and 104 columns
[2] LGG_CNASNP-20160128: RaggedExperiment with 411918 rows and 1015 columns
[3] LGG_CNVSNP-20160128: RaggedExperiment with 79791 rows and 1015 columns
[4] LGG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[5] LGG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 46 rows and 513 columns
[6] LGG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[7] LGG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 526 columns
[8] LGG_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 27 columns
[9] LGG_Mutation-20160128: RaggedExperiment with 9885 rows and 286 columns
[10] LGG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 530 columns
[11] LGG_RPPAArray-20160128: SummarizedExperiment with 201 rows and 435 columns
[12] LGG_Methylation-20160128: SummarizedExperiment with 485577 rows and 530 columns
> rownames( LGG )
CharacterList of length 12
[["LGG_CNASeq-20160128"]] character(0)
[["LGG_CNASNP-20160128"]] character(0)
[["LGG_CNVSNP-20160128"]] character(0)
[["LGG_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["LGG_GISTIC_Peaks-20160128"]] chr1:3814904-5625565 ...
[["LGG_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LGG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LGG_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LGG_Mutation-20160128"]] character(0)
[["LGG_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( LGG )
CharacterList of length 12
[["LGG_CNASeq-20160128"]] TCGA-CS-4938-01B-11D-1891-02 ...
[["LGG_CNASNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_CNVSNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_AllByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_Peaks-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_ThresholdedByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_miRNASeqGene-20160128"]] TCGA-CS-4938-01B-11R-1895-13 ...
[["LGG_mRNAArray-20160128"]] TCGA-CS-4942-01A-01R-1470-07 ...
[["LGG_Mutation-20160128"]] TCGA-CS-4938-01B-11D-1893-08 ...
[["LGG_RNASeq2GeneNorm-20160128"]] TCGA-CS-4938-01B-11R-1896-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LGG_CNASeq-20160128 0.2 Mb
2 LGG_CNASNP-20160128 11.3 Mb
3 LGG_CNVSNP-20160128 2.4 Mb
4 LGG_GISTIC_AllByGene-20160128 4.9 Mb
5 LGG_GISTIC_Peaks-20160128 0.1 Mb
6 LGG_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LGG_miRNASeqGene-20160128 0.1 Mb
8 LGG_mRNAArray-20160128 1.1 Mb
9 LGG_Mutation-20160128 4.2 Mb
10 LGG_RNASeq2GeneNorm-20160128 1.3 Mb
11 LGG_RPPAArray-20160128 0.1 Mb
12 LGG_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
391 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
125.00 125.00 2.23 1.87 2.83
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.00 32.00 41.00 42.93 53.00 86.00 2
vital_status:
0 1 NA's
389 126 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7 438 814 1219 1547 5166 391
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-1.0 384.0 629.0 880.1 1147.0 6423.0 127
tumor_tissue_site:
central nervous system NA's
515 1
gender:
female male NA's
230 285 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2008 2011 2009 2012 2013 1
radiation_therapy:
no yes NA's
186 296 34
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 80.00 90.00 86.64 100.00 100.00 209
histological_type:
astrocytoma oligoastrocytoma oligodendroglioma NA's
194 130 191 1
race:
american indian or alaska native asian
1 8
black or african american white
21 475
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
32 449 35
Including an additional 1764 columns
A document describing the TCGA cancer code
> experiments( LIHC )
ExperimentList class object of length 11:
[1] LIHC_CNASNP-20160128: RaggedExperiment with 363628 rows and 760 columns
[2] LIHC_CNVSNP-20160128: RaggedExperiment with 93328 rows and 760 columns
[3] LIHC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[4] LIHC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 59 rows and 370 columns
[5] LIHC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[6] LIHC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns
[7] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
[8] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 423 columns
[9] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns
[10] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns
[11] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns
> rownames( LIHC )
CharacterList of length 11
[["LIHC_CNASNP-20160128"]] character(0)
[["LIHC_CNVSNP-20160128"]] character(0)
[["LIHC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LIHC_GISTIC_Peaks-20160128"]] chr1:1-6847369 ... chr22:44205320-51304566
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LIHC_Mutation-20160128"]] character(0)
[["LIHC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( LIHC )
CharacterList of length 11
[["LIHC_CNASNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_CNVSNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_AllByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_Peaks-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ...
[["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ...
[["LIHC_RNASeq2GeneNorm-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ...
[["LIHC_RNASeqGene-20160128"]] TCGA-BC-4073-01B-02R-A131-07 ...
[["LIHC_RPPAArray-20160128"]] TCGA-BC-4072-01B-21-A40L-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 LIHC_CNASNP-20160128 9.9 Mb
2 LIHC_CNVSNP-20160128 2.7 Mb
3 LIHC_GISTIC_AllByGene-20160128 4.9 Mb
4 LIHC_GISTIC_Peaks-20160128 0.1 Mb
5 LIHC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 LIHC_miRNASeqGene-20160128 0.1 Mb
7 LIHC_Mutation-20160128 16.8 Mb
8 LIHC_RNASeq2GeneNorm-20160128 1.3 Mb
9 LIHC_RNASeqGene-20160128 1.3 Mb
10 LIHC_RPPAArray-20160128 0 Mb
11 LIHC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
245 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
132.000 132.000 1.144 0.956 1.633
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16.00 51.00 61.00 59.27 69.00 87.00 4
vital_status:
0 1
245 132
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 194.8 417.5 672.1 837.0 3258.0 245
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 395.8 649.5 885.8 1222.0 3675.0 133
tumor_tissue_site:
liver
377
pathology_N_stage:
n0 n1 nx NA's
257 4 115 1
pathology_M_stage:
m0 m1 mx
272 4 101
gender:
female male
122 255
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2008 2011 2010 2012 2013 3
radiation_therapy:
no yes NA's
345 9 23
histological_type:
fibrolamellar carcinoma hepatocellular carcinoma
3 367
hepatocholangiocarcinoma (mixed)
7
residual_tumor:
r0 r1 r2 rx NA's
330 17 1 22 7
race:
american indian or alaska native asian
2 161
black or african american white
17 187
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
18 340 19
Including an additional 1218 columns
A document describing the TCGA cancer code
> experiments( LUAD )
ExperimentList class object of length 14:
[1] LUAD_CNASeq-20160128: RaggedExperiment with 399592 rows and 249 columns
[2] LUAD_CNASNP-20160128: RaggedExperiment with 501475 rows and 1095 columns
[3] LUAD_CNVSNP-20160128: RaggedExperiment with 115836 rows and 1095 columns
[4] LUAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[5] LUAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 73 rows and 516 columns
[6] LUAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[7] LUAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 498 columns
[8] LUAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 32 columns
[9] LUAD_Mutation-20160128: RaggedExperiment with 72541 rows and 230 columns
[10] LUAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 576 columns
[11] LUAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 162 columns
[12] LUAD_RPPAArray-20160128: SummarizedExperiment with 223 rows and 365 columns
[13] LUAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 89 columns
[14] LUAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 492 columns
> rownames( LUAD )
CharacterList of length 14
[["LUAD_CNASeq-20160128"]] character(0)
[["LUAD_CNASNP-20160128"]] character(0)
[["LUAD_CNVSNP-20160128"]] character(0)
[["LUAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LUAD_GISTIC_Peaks-20160128"]] chr1:1-32049393 ... chr22:46723702-51304566
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LUAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LUAD_Mutation-20160128"]] character(0)
[["LUAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( LUAD )
CharacterList of length 14
[["LUAD_CNASeq-20160128"]] TCGA-05-4249-01A-01D-1103-02 ...
[["LUAD_CNASNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_CNVSNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_AllByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_Peaks-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_miRNASeqGene-20160128"]] TCGA-05-4384-01A-01T-1754-13 ...
[["LUAD_mRNAArray-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
[["LUAD_Mutation-20160128"]] TCGA-05-4249-01A-01D-1105-08 ...
[["LUAD_RNASeq2GeneNorm-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUAD_CNASeq-20160128 10.8 Mb
2 LUAD_CNASNP-20160128 13.7 Mb
3 LUAD_CNVSNP-20160128 3.4 Mb
4 LUAD_GISTIC_AllByGene-20160128 4.9 Mb
5 LUAD_GISTIC_Peaks-20160128 0.1 Mb
6 LUAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LUAD_miRNASeqGene-20160128 0.1 Mb
8 LUAD_mRNAArray-20160128 1.1 Mb
9 LUAD_Mutation-20160128 92.9 Mb
10 LUAD_RNASeq2GeneNorm-20160128 1.3 Mb
11 LUAD_RNASeqGene-20160128 1.3 Mb
12 LUAD_RPPAArray-20160128 0.1 Mb
13 LUAD_Methylation_methyl27-20160128 4.9 Mb
14 LUAD_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
336 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
184.00 184.00 1.70 1.37 2.00
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
33.00 59.00 66.00 65.22 72.00 88.00 31
vital_status:
0 1
332 188
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 297.8 619.0 791.4 1120.0 4961.0 336
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 459.5 670.0 968.7 1139.0 7248.0 193
tumor_tissue_site:
lung
520
gender:
female male
279 241
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1991 2007 2010 2008 2011 2013 19
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 96.5 141.0 327.6 386.0 1178.0 513
radiation_therapy:
no yes NA's
413 61 46
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 78.55 100.00 100.00 382
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.50 40.00 41.79 50.00 154.00 165
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1930 1956 1965 1965 1972 1999 241
residual_tumor:
r0 r1 r2 rx NA's
347 13 4 26 130
race:
american indian or alaska native asian
1 8
black or african american white
53 392
NA's
66
ethnicity:
hispanic or latino not hispanic or latino NA's
7 388 125
Including an additional 2607 columns
A document describing the TCGA cancer code
> experiments( LUSC )
ExperimentList class object of length 16:
[1] LUSC_CNACGH-20160128: RaggedExperiment with 87417 rows and 407 columns
[2] LUSC_CNASNP-20160128: RaggedExperiment with 543091 rows and 1035 columns
[3] LUSC_CNVSNP-20160128: RaggedExperiment with 134864 rows and 1032 columns
[4] LUSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[5] LUSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 78 rows and 501 columns
[6] LUSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[7] LUSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 387 columns
[8] LUSC_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 112 columns
[9] LUSC_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 154 columns
[10] LUSC_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 133 columns
[11] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
[12] LUSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 552 columns
[13] LUSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 240 columns
[14] LUSC_RPPAArray-20160128: SummarizedExperiment with 223 rows and 328 columns
[15] LUSC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 160 columns
[16] LUSC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 412 columns
> rownames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] character(0)
[["LUSC_CNASNP-20160128"]] character(0)
[["LUSC_CNVSNP-20160128"]] character(0)
[["LUSC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["LUSC_GISTIC_Peaks-20160128"]] chr1:1-31262836 ... chr22:45736500-51304566
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["LUSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUSC_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["LUSC_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] AACS FSTL1 ELMO2 ... CTSC AQP7
...
<6 more elements>
> colnames( LUSC )
CharacterList of length 16
[["LUSC_CNACGH-20160128"]] TCGA-18-3406-01A-01D-1519-02 ...
[["LUSC_CNASNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_CNVSNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_AllByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_Peaks-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_miRNASeqGene-20160128"]] TCGA-18-5592-01A-01T-1634-13 ...
[["LUSC_mRNAArray_huex-20160128"]] TCGA-18-3406-01A-01R-1030-03 ...
[["LUSC_mRNAArray_TX_g4502a-20160128"]] TCGA-18-3406-01A-01R-0980-07 ...
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] TCGA-18-3406-01A-01R-1031-01 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUSC_CNACGH-20160128 2.5 Mb
2 LUSC_CNASNP-20160128 14.8 Mb
3 LUSC_CNVSNP-20160128 3.9 Mb
4 LUSC_GISTIC_AllByGene-20160128 4.9 Mb
5 LUSC_GISTIC_Peaks-20160128 0.1 Mb
6 LUSC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 LUSC_miRNASeqGene-20160128 0.1 Mb
8 LUSC_mRNAArray_huex-20160128 1.2 Mb
9 LUSC_mRNAArray_TX_g4502a-20160128 1.1 Mb
10 LUSC_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb
11 LUSC_Mutation-20160128 81 Mb
12 LUSC_RNASeq2GeneNorm-20160128 1.3 Mb
13 LUSC_RNASeqGene-20160128 1.3 Mb
14 LUSC_RPPAArray-20160128 0 Mb
15 LUSC_Methylation_methyl27-20160128 4.9 Mb
16 LUSC_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
289 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
215.00 215.00 1.51 1.25 1.88
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
39.00 62.00 68.00 67.26 73.00 90.00 10
vital_status:
0 1
284 220
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.0 280.0 550.0 872.3 1110.5 5287.0 289
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 394 757 1049 1374 4765 221
tumor_tissue_site:
lung
504
pathology_N_stage:
n0 n1 n2 n3 nx
320 133 40 5 6
gender:
female male
131 373
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2005 2009 2008 2011 2013 25
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 298.8 706.0 904.8 1051.8 3724.0 436
radiation_therapy:
no yes NA's
387 53 64
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 0.0 80.0 60.3 90.0 100.0 338
histological_type:
lung basaloid squamous cell carcinoma
15
lung papillary squamous cell caricnoma
6
lung small cell squamous cell carcinoma
1
lung squamous cell carcinoma- not otherwise specified (nos)
482
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 31.12 50.00 52.91 64.50 240.00 77
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1933 1952 1960 1960 1968 1997 183
residual_tumor:
r0 r1 r2 rx NA's
401 12 4 23 64
race:
asian black or african american white
9 31 351
NA's
113
ethnicity:
hispanic or latino not hispanic or latino NA's
8 319 177
Including an additional 2238 columns
A document describing the TCGA cancer code
> experiments( MESO )
ExperimentList class object of length 9:
[1] MESO_CNASNP-20160128: RaggedExperiment with 90003 rows and 173 columns
[2] MESO_CNVSNP-20160128: RaggedExperiment with 18335 rows and 172 columns
[3] MESO_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[4] MESO_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 87 columns
[5] MESO_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[6] MESO_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 87 columns
[7] MESO_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 87 columns
[8] MESO_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[9] MESO_Methylation-20160128: SummarizedExperiment with 485577 rows and 87 columns
> rownames( MESO )
CharacterList of length 9
[["MESO_CNASNP-20160128"]] character(0)
[["MESO_CNVSNP-20160128"]] character(0)
[["MESO_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["MESO_GISTIC_Peaks-20160128"]] chr1:1-31262836 ... chr22:29969457-30128393
[["MESO_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["MESO_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["MESO_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["MESO_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( MESO )
CharacterList of length 9
[["MESO_CNASNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_CNVSNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_AllByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_Peaks-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_ThresholdedByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_miRNASeqGene-20160128"]] TCGA-3H-AB3K-01A-11R-A404-13 ...
[["MESO_RNASeq2GeneNorm-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RPPAArray-20160128"]] TCGA-3H-AB3K-01A-21-A45O-20 ...
[["MESO_Methylation-20160128"]] TCGA-3H-AB3K-01A-11D-A39S-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 MESO_CNASNP-20160128 2.5 Mb
2 MESO_CNVSNP-20160128 0.6 Mb
3 MESO_GISTIC_AllByGene-20160128 4.9 Mb
4 MESO_GISTIC_Peaks-20160128 0 Mb
5 MESO_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 MESO_miRNASeqGene-20160128 0.1 Mb
7 MESO_RNASeq2GeneNorm-20160128 1.3 Mb
8 MESO_RPPAArray-20160128 0 Mb
9 MESO_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
14 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
73.00 73.00 1.25 1.11 1.67
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 57.00 64.00 62.99 69.00 81.00
vital_status:
0 1
13 74
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 253.0 457.0 584.1 789.0 2790.0 14
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-8 499 1168 1091 1490 2359 74
tumor_tissue_site:
pleura
87
pathology_N_stage:
n0 n1 n2 n3 nx
44 10 26 3 4
pathology_M_stage:
m0 m1 mx
57 3 27
gender:
female male
16 71
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2008 2010 2009 2012 2013
radiation_therapy:
no yes NA's
62 24 1
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 77.65 90.00 100.00 70
histological_type:
biphasic mesothelioma diffuse malignant mesothelioma - nos
23 5
epithelioid mesothelioma sarcomatoid mesothelioma
57 2
residual_tumor:
r0 r1 r2 rx NA's
17 3 15 11 41
race:
asian black or african american white
1 1 85
ethnicity:
not hispanic or latino NA's
73 14
Including an additional 636 columns
A document describing the TCGA cancer code
> experiments( OV )
ExperimentList class object of length 19:
[1] OV_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 128946 rows and 472 columns
[2] OV_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 245847 rows and 674 columns
[3] OV_CNASNP-20160128: RaggedExperiment with 907765 rows and 1145 columns
[4] OV_CNVSNP-20160128: RaggedExperiment with 261680 rows and 1141 columns
[5] OV_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[6] OV_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 573 columns
[7] OV_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[8] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns
[9] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns
[10] OV_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 575 columns
[11] OV_mRNAArray_TX_g4502a_1-20160128: SummarizedExperiment with 17814 rows and 546 columns
[12] OV_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 31 columns
[13] OV_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 524 columns
[14] OV_Mutation-20160128: RaggedExperiment with 20219 rows and 316 columns
[15] OV_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 307 columns
[16] OV_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 299 columns
[17] OV_RPPAArray-20160128: SummarizedExperiment with 208 rows and 427 columns
[18] OV_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 591 columns
[19] OV_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 10 columns
> rownames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["OV_CNASNP-20160128"]] character(0)
[["OV_CNVSNP-20160128"]] character(0)
[["OV_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["OV_GISTIC_Peaks-20160128"]] chr1:26963410-27570286 ...
[["OV_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["OV_miRNAArray-20160128"]] DarkCorner dmr_285 ... NegativeControl SCorner3
[["OV_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["OV_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
...
<9 more elements>
> colnames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] TCGA-04-1331-01A-01D-0431-02 ...
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-04-1353-01A-01D-1046-02 ...
[["OV_CNASNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_CNVSNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_AllByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_Peaks-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_ThresholdedByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_miRNAArray-20160128"]] TCGA-04-1331-01A-01T-0438-07 ...
[["OV_miRNASeqGene-20160128"]] TCGA-04-1331-01A-01R-1569-13 ...
[["OV_mRNAArray_huex-20160128"]] TCGA-04-1331-01A-01R-0435-03 ...
...
<9 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 OV_CNACGH_CGH_hg_244a-20160128 3.6 Mb
2 OV_CNACGH_CGH_hg_415k_g4124a-20160128 6.8 Mb
3 OV_CNASNP-20160128 24.6 Mb
4 OV_CNVSNP-20160128 7.3 Mb
5 OV_GISTIC_AllByGene-20160128 4.9 Mb
6 OV_GISTIC_Peaks-20160128 0.1 Mb
7 OV_GISTIC_ThresholdedByGene-20160128 4.9 Mb
8 OV_miRNAArray-20160128 0.1 Mb
9 OV_miRNASeqGene-20160128 0.1 Mb
10 OV_mRNAArray_huex-20160128 1.2 Mb
11 OV_mRNAArray_TX_g4502a_1-20160128 1.2 Mb
12 OV_mRNAArray_TX_g4502a-20160128 1.1 Mb
13 OV_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb
14 OV_Mutation-20160128 10.3 Mb
15 OV_RNASeq2GeneNorm-20160128 1.3 Mb
16 OV_RNASeqGene-20160128 1.3 Mb
17 OV_RPPAArray-20160128 0.1 Mb
18 OV_Methylation_methyl27-20160128 4.9 Mb
19 OV_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
343.00 343.00 2.94 2.76 3.17
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.78 69.00 89.00 21
vital_status:
0 1
246 344
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 567.5 1073.0 1147.4 1557.0 4624.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16 266 842 1216 1931 5481 358
tumor_tissue_site:
omentum ovary peritoneum ovary NA's
3 575 2 10
gender:
female NA's
580 10
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2001 2004 2004 2007 2013 10
radiation_therapy:
no yes NA's
556 5 29
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 60.00 80.00 75.83 80.00 100.00 506
histological_type:
serous cystadenocarcinoma NA's
580 10
residual_tumor:
r0 r1 r2 rx NA's
15 31 5 3 536
ethnicity:
hispanic or latino not hispanic or latino NA's
11 338 241
Including an additional 2869 columns
A document describing the TCGA cancer code
> experiments( PAAD )
ExperimentList class object of length 10:
[1] PAAD_CNASNP-20160128: RaggedExperiment with 203871 rows and 368 columns
[2] PAAD_CNVSNP-20160128: RaggedExperiment with 34808 rows and 365 columns
[3] PAAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[4] PAAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 52 rows and 184 columns
[5] PAAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[6] PAAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 183 columns
[7] PAAD_Mutation-20160128: RaggedExperiment with 30357 rows and 150 columns
[8] PAAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 183 columns
[9] PAAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 123 columns
[10] PAAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 195 columns
> rownames( PAAD )
CharacterList of length 10
[["PAAD_CNASNP-20160128"]] character(0)
[["PAAD_CNVSNP-20160128"]] character(0)
[["PAAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["PAAD_GISTIC_Peaks-20160128"]] chr1:26795113-27650365 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["PAAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PAAD_Mutation-20160128"]] character(0)
[["PAAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PAAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PAAD_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( PAAD )
CharacterList of length 10
[["PAAD_CNASNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_CNVSNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_AllByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_Peaks-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_miRNASeqGene-20160128"]] TCGA-2J-AAB1-01A-11R-A41G-13 ...
[["PAAD_Mutation-20160128"]] TCGA-2J-AAB1-01A-11D-A40W-08 ...
[["PAAD_RNASeq2GeneNorm-20160128"]] TCGA-2J-AAB1-01A-11R-A41B-07 ...
[["PAAD_RPPAArray-20160128"]] TCGA-2J-AAB4-01A-21-A43K-20 ...
[["PAAD_Methylation-20160128"]] TCGA-2J-AAB1-01A-11D-A40Y-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 PAAD_CNASNP-20160128 5.6 Mb
2 PAAD_CNVSNP-20160128 1 Mb
3 PAAD_GISTIC_AllByGene-20160128 4.9 Mb
4 PAAD_GISTIC_Peaks-20160128 0.1 Mb
5 PAAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 PAAD_miRNASeqGene-20160128 0.1 Mb
7 PAAD_Mutation-20160128 111 Mb
8 PAAD_RNASeq2GeneNorm-20160128 1.3 Mb
9 PAAD_RPPAArray-20160128 0 Mb
10 PAAD_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
85 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
100.000 100.000 1.079 0.967 1.315
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
35.00 57.00 65.00 64.86 73.00 88.00
vital_status:
0 1
85 100
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
12.0 228.5 394.0 459.5 596.5 2182.0 85
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 338.0 517.0 692.4 951.0 2741.0 100
tumor_tissue_site:
pancreas
185
pathology_N_stage:
n0 n1 n1b nx NA's
50 126 4 4 1
pathology_M_stage:
m0 m1 mx
85 5 95
gender:
female male
83 102
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2001 2010 2012 2011 2012 2013 1
radiation_therapy:
no yes NA's
125 45 15
histological_type:
pancreas-adenocarcinoma ductal type
154
pancreas-adenocarcinoma-other subtype
25
pancreas-colloid (mucinous non-cystic) carcinoma
4
pancreas-undifferentiated carcinoma
1
NA's
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.30 15.00 25.00 26.84 40.00 75.00 128
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1948 1960 1971 1971 1982 1993 138
residual_tumor:
r0 r1 r2 rx NA's
111 53 5 4 12
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 2.000 2.989 4.000 16.000 4
race:
asian black or african american white
11 7 162
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
5 137 43
Including an additional 960 columns
A document describing the TCGA cancer code
> experiments( PCPG )
ExperimentList class object of length 10:
[1] PCPG_CNASNP-20160128: RaggedExperiment with 297329 rows and 360 columns
[2] PCPG_CNVSNP-20160128: RaggedExperiment with 31256 rows and 346 columns
[3] PCPG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[4] PCPG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 27 rows and 162 columns
[5] PCPG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[6] PCPG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 187 columns
[7] PCPG_Mutation-20160128: RaggedExperiment with 4662 rows and 184 columns
[8] PCPG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 187 columns
[9] PCPG_RPPAArray-20160128: SummarizedExperiment with 192 rows and 82 columns
[10] PCPG_Methylation-20160128: SummarizedExperiment with 485577 rows and 187 columns
> rownames( PCPG )
CharacterList of length 10
[["PCPG_CNASNP-20160128"]] character(0)
[["PCPG_CNVSNP-20160128"]] character(0)
[["PCPG_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["PCPG_GISTIC_Peaks-20160128"]] chr1:117751737-118152240 ...
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["PCPG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PCPG_Mutation-20160128"]] character(0)
[["PCPG_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PCPG_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PCPG_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( PCPG )
CharacterList of length 10
[["PCPG_CNASNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_CNVSNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_GISTIC_AllByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_Peaks-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_miRNASeqGene-20160128"]] TCGA-P7-A5NX-01A-11R-A35M-13 ...
[["PCPG_Mutation-20160128"]] TCGA-P7-A5NX-01A-11D-A35D-08 ...
[["PCPG_RNASeq2GeneNorm-20160128"]] TCGA-P7-A5NX-01A-11R-A35K-07 ...
[["PCPG_RPPAArray-20160128"]] TCGA-P7-A5NX-01A-21-A43B-20 ...
[["PCPG_Methylation-20160128"]] TCGA-P7-A5NX-01A-11D-A35E-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 PCPG_CNASNP-20160128 8.1 Mb
2 PCPG_CNVSNP-20160128 0.9 Mb
3 PCPG_GISTIC_AllByGene-20160128 4.9 Mb
4 PCPG_GISTIC_Peaks-20160128 0 Mb
5 PCPG_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 PCPG_miRNASeqGene-20160128 0.1 Mb
7 PCPG_Mutation-20160128 8.4 Mb
8 PCPG_RNASeq2GeneNorm-20160128 1.3 Mb
9 PCPG_RPPAArray-20160128 0 Mb
10 PCPG_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
173 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
6.00 6.00 1.24 0.26 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
19.00 35.00 46.00 47.33 58.50 83.00
vital_status:
0 1
173 6
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
88.0 148.5 452.5 901.0 715.2 3563.0 173
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2 352 766 1071 1301 9634 6
tumor_tissue_site:
adrenal gland extra-adrenal site
147 32
gender:
female male
101 78
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1988 2009 2011 2010 2012 2013
radiation_therapy:
no yes NA's
172 5 2
karnofsky_performance_score:
70 80 90 100 NA's
1 2 13 46 117
histological_type:
paraganglioma
18
paraganglioma; extra-adrenal pheochromocytoma
13
pheochromocytoma
148
number_of_lymph_nodes:
0 1 2 13 NA's
16 3 1 1 158
race:
american indian or alaska native asian
1 6
black or african american white
20 148
NA's
4
ethnicity:
hispanic or latino not hispanic or latino NA's
5 138 36
Including an additional 894 columns
A document describing the TCGA cancer code
> experiments( PRAD )
ExperimentList class object of length 11:
[1] PRAD_CNASeq-20160128: RaggedExperiment with 23398 rows and 230 columns
[2] PRAD_CNASNP-20160128: RaggedExperiment with 573776 rows and 1029 columns
[3] PRAD_CNVSNP-20160128: RaggedExperiment with 117345 rows and 1023 columns
[4] PRAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[5] PRAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 58 rows and 492 columns
[6] PRAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[7] PRAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 547 columns
[8] PRAD_Mutation-20160128: RaggedExperiment with 12348 rows and 332 columns
[9] PRAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 550 columns
[10] PRAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 352 columns
[11] PRAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 549 columns
> rownames( PRAD )
CharacterList of length 11
[["PRAD_CNASeq-20160128"]] character(0)
[["PRAD_CNASNP-20160128"]] character(0)
[["PRAD_CNVSNP-20160128"]] character(0)
[["PRAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["PRAD_GISTIC_Peaks-20160128"]] chr1:63901623-66226788 ...
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["PRAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PRAD_Mutation-20160128"]] character(0)
[["PRAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PRAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( PRAD )
CharacterList of length 11
[["PRAD_CNASeq-20160128"]] TCGA-CH-5741-01A-11D-1572-02 ...
[["PRAD_CNASNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_CNVSNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_AllByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_Peaks-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_miRNASeqGene-20160128"]] TCGA-2A-A8VL-01A-21R-A37H-13 ...
[["PRAD_Mutation-20160128"]] TCGA-2A-A8VL-01A-21D-A377-08 ...
[["PRAD_RNASeq2GeneNorm-20160128"]] TCGA-2A-A8VL-01A-21R-A37L-07 ...
[["PRAD_RPPAArray-20160128"]] TCGA-2A-A8VL-01A-11-A43M-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 PRAD_CNASeq-20160128 0.7 Mb
2 PRAD_CNASNP-20160128 15.6 Mb
3 PRAD_CNVSNP-20160128 3.4 Mb
4 PRAD_GISTIC_AllByGene-20160128 4.9 Mb
5 PRAD_GISTIC_Peaks-20160128 0.1 Mb
6 PRAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 PRAD_miRNASeqGene-20160128 0.1 Mb
8 PRAD_Mutation-20160128 21.5 Mb
9 PRAD_RNASeq2GeneNorm-20160128 1.3 Mb
10 PRAD_RPPAArray-20160128 0 Mb
11 PRAD_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
488 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
10.00 10.00 3.02 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
41.00 56.00 61.00 61.02 66.00 78.00 11
vital_status:
0 1
488 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
146.0 743.8 1102.0 1579.0 2315.5 3502.0 488
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
23.0 523.5 926.0 1076.5 1458.0 5024.0 10
tumor_tissue_site:
prostate
498
pathology_N_stage:
n0 n1 NA's
346 79 73
gender:
male
498
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2009 2011 2010 2012 2013 31
radiation_therapy:
no yes NA's
395 59 44
histological_type:
prostate adenocarcinoma acinar type prostate adenocarcinoma, other subtype
483 15
residual_tumor:
r0 r1 r2 rx NA's
316 147 5 15 15
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.4447 0.0000 15.0000 91
gleason_score:
6 7 8 9 10
45 248 64 137 4
psa_value:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.030 0.100 1.742 0.110 323.000 57
days_to_psa:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-164.0 191.0 512.0 685.6 926.0 3447.0 53
race:
asian black or african american white
2 7 147
NA's
342
ethnicity:
not hispanic or latino NA's
152 346
Including an additional 1126 columns
A document describing the TCGA cancer code
> experiments( READ )
ExperimentList class object of length 14:
[1] READ_CNASeq-20160128: RaggedExperiment with 56380 rows and 70 columns
[2] READ_CNASNP-20160128: RaggedExperiment with 156806 rows and 316 columns
[3] READ_CNVSNP-20160128: RaggedExperiment with 35765 rows and 316 columns
[4] READ_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[5] READ_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 55 rows and 165 columns
[6] READ_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[7] READ_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 76 columns
[8] READ_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[9] READ_Mutation-20160128: RaggedExperiment with 22075 rows and 69 columns
[10] READ_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 72 columns
[11] READ_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 72 columns
[12] READ_RPPAArray-20160128: SummarizedExperiment with 208 rows and 131 columns
[13] READ_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[14] READ_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 106 columns
> rownames( READ )
CharacterList of length 14
[["READ_CNASeq-20160128"]] character(0)
[["READ_CNASNP-20160128"]] character(0)
[["READ_CNVSNP-20160128"]] character(0)
[["READ_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["READ_GISTIC_Peaks-20160128"]] chr1:3814904-31841618 ...
[["READ_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["READ_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["READ_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["READ_Mutation-20160128"]] character(0)
[["READ_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( READ )
CharacterList of length 14
[["READ_CNASeq-20160128"]] TCGA-AF-2691-01A-01D-1167-02 ...
[["READ_CNASNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_CNVSNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_AllByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_Peaks-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_ThresholdedByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_miRNASeqGene-20160128"]] TCGA-AF-2687-01A-02T-1735-13 ...
[["READ_mRNAArray-20160128"]] TCGA-AF-2689-11A-01R-1758-07 ...
[["READ_Mutation-20160128"]] TCGA-AF-2689-01A-01W-0831-10 ... TCGA-AG-A036-01
[["READ_RNASeq2GeneNorm-20160128"]] TCGA-AF-2691-01A-01R-0821-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 READ_CNASeq-20160128 1.5 Mb
2 READ_CNASNP-20160128 4.3 Mb
3 READ_CNVSNP-20160128 1.1 Mb
4 READ_GISTIC_AllByGene-20160128 4.9 Mb
5 READ_GISTIC_Peaks-20160128 0.1 Mb
6 READ_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 READ_miRNASeqGene-20160128 0.1 Mb
8 READ_mRNAArray-20160128 1.1 Mb
9 READ_Mutation-20160128 9.6 Mb
10 READ_RNASeq2GeneNorm-20160128 1.3 Mb
11 READ_RNASeqGene-20160128 1.3 Mb
12 READ_RPPAArray-20160128 0 Mb
13 READ_Methylation_methyl27-20160128 4.9 Mb
14 READ_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
142 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
27.00 27.00 2.00 1.44 3.25
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
31.00 57.00 66.00 64.37 72.00 90.00
vital_status:
0 1
141 28
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
59.0 347.5 730.0 786.1 1193.0 1741.0 142
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 366.0 625.0 779.5 1096.0 3932.0 28
tumor_tissue_site:
rectum NA's
166 3
pathology_M_stage:
m0 m1 m1a mx NA's
128 22 2 14 3
gender:
female male
77 92
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2007 2009 2008 2010 2012
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.0 292.2 863.0 1420.1 2214.5 3667.0 161
radiation_therapy:
no yes NA's
114 22 33
histological_type:
rectal adenocarcinoma rectal mucinous adenocarcinoma
150 13
NA's
6
tumor_stage:
stage iia NA's
1 168
residual_tumor:
r0 r1 r2 rx NA's
126 2 12 5 24
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.692 3.000 31.000 10
ethnicity:
hispanic or latino not hispanic or latino NA's
1 84 84
Including an additional 2242 columns
A document describing the TCGA cancer code
> experiments( SARC )
ExperimentList class object of length 10:
[1] SARC_CNASNP-20160128: RaggedExperiment with 337377 rows and 516 columns
[2] SARC_CNVSNP-20160128: RaggedExperiment with 106739 rows and 513 columns
[3] SARC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[4] SARC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 64 rows and 257 columns
[5] SARC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[6] SARC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 263 columns
[7] SARC_Mutation-20160128: RaggedExperiment with 20376 rows and 247 columns
[8] SARC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 265 columns
[9] SARC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 226 columns
[10] SARC_Methylation-20160128: SummarizedExperiment with 485577 rows and 269 columns
> rownames( SARC )
CharacterList of length 10
[["SARC_CNASNP-20160128"]] character(0)
[["SARC_CNVSNP-20160128"]] character(0)
[["SARC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["SARC_GISTIC_Peaks-20160128"]] chr1:1-5923787 ... chr22:45095899-51304566
[["SARC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["SARC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SARC_Mutation-20160128"]] character(0)
[["SARC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["SARC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["SARC_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( SARC )
CharacterList of length 10
[["SARC_CNASNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_CNVSNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_AllByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_Peaks-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_miRNASeqGene-20160128"]] TCGA-3B-A9HI-01A-11R-A38N-13 ...
[["SARC_Mutation-20160128"]] TCGA-3B-A9HI-01A-11D-A387-09 ...
[["SARC_RNASeq2GeneNorm-20160128"]] TCGA-3B-A9HI-01A-11R-A38C-07 ...
[["SARC_RPPAArray-20160128"]] TCGA-3B-A9HI-01A-21-A456-20 ...
[["SARC_Methylation-20160128"]] TCGA-3B-A9HI-01A-11D-A388-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 SARC_CNASNP-20160128 9.2 Mb
2 SARC_CNVSNP-20160128 3 Mb
3 SARC_GISTIC_AllByGene-20160128 4.9 Mb
4 SARC_GISTIC_Peaks-20160128 0.1 Mb
5 SARC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 SARC_miRNASeqGene-20160128 0.1 Mb
7 SARC_Mutation-20160128 19.5 Mb
8 SARC_RNASeq2GeneNorm-20160128 1.3 Mb
9 SARC_RPPAArray-20160128 0 Mb
10 SARC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
162 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
99.00 99.00 1.78 1.51 2.46
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 53.00 61.00 60.88 71.00 90.00 1
vital_status:
0 1
162 99
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.0 322.5 648.0 863.6 1169.5 2694.0 162
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.0 585.8 1092.0 1391.1 1891.8 5723.0 99
gender:
female male
142 119
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2007 2010 2009 2012 2013 4
radiation_therapy:
no yes NA's
181 74 6
residual_tumor:
r0 r1 r2 rx NA's
155 70 9 26 1
race:
asian black or african american white
6 18 228
NA's
9
ethnicity:
hispanic or latino not hispanic or latino NA's
5 223 33
Including an additional 1413 columns
A document describing the TCGA cancer code
> experiments( SKCM )
ExperimentList class object of length 11:
[1] SKCM_CNASeq-20160128: RaggedExperiment with 31416 rows and 238 columns
[2] SKCM_CNASNP-20160128: RaggedExperiment with 452114 rows and 938 columns
[3] SKCM_CNVSNP-20160128: RaggedExperiment with 108084 rows and 937 columns
[4] SKCM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[5] SKCM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 53 rows and 367 columns
[6] SKCM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[7] SKCM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 452 columns
[8] SKCM_Mutation-20160128: RaggedExperiment with 290322 rows and 345 columns
[9] SKCM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 473 columns
[10] SKCM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 355 columns
[11] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns
> rownames( SKCM )
CharacterList of length 11
[["SKCM_CNASeq-20160128"]] character(0)
[["SKCM_CNASNP-20160128"]] character(0)
[["SKCM_CNVSNP-20160128"]] character(0)
[["SKCM_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["SKCM_GISTIC_Peaks-20160128"]] chr1:1-6847369 ... chr22:41468899-41849552
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["SKCM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SKCM_Mutation-20160128"]] character(0)
[["SKCM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["SKCM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( SKCM )
CharacterList of length 11
[["SKCM_CNASeq-20160128"]] TCGA-BF-A1PU-01A-11D-A18Z-02 ...
[["SKCM_CNASNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_CNVSNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_AllByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_Peaks-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_miRNASeqGene-20160128"]] TCGA-3N-A9WC-06A-11R-A38N-13 ...
[["SKCM_Mutation-20160128"]] TCGA-BF-A1PU-01A-11D-A19A-08 ...
[["SKCM_RNASeq2GeneNorm-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
[["SKCM_RPPAArray-20160128"]] TCGA-3N-A9WC-06A-21-A444-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 SKCM_CNASeq-20160128 0.9 Mb
2 SKCM_CNASNP-20160128 12.3 Mb
3 SKCM_CNVSNP-20160128 3.2 Mb
4 SKCM_GISTIC_AllByGene-20160128 4.9 Mb
5 SKCM_GISTIC_Peaks-20160128 0.1 Mb
6 SKCM_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 SKCM_miRNASeqGene-20160128 0.1 Mb
8 SKCM_Mutation-20160128 299.6 Mb
9 SKCM_RNASeq2GeneNorm-20160128 1.3 Mb
10 SKCM_RPPAArray-20160128 0 Mb
11 SKCM_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
249 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
221.00 221.00 2.99 2.40 3.90
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.00 48.00 58.00 58.24 71.00 90.00 8
vital_status:
0 1
247 223
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
79 518 1093 1789 2073 10870 249
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2.0 477.5 1146.0 1885.3 2658.8 11252.0 230
days_to_submitted_specimen_dx:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2 0 344 1017 1372 10847 14
melanoma_ulceration:
no yes NA's
146 167 157
melanoma_primary_known:
no yes
47 423
Breslow_thickness:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.300 3.000 5.585 6.950 75.000 111
gender:
female male
180 290
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1978 2003 2008 2006 2011 2013 11
radiation_therapy:
no yes NA's
420 49 1
race:
asian black or african american white
12 1 447
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
11 446 13
Including an additional 1517 columns
A document describing the TCGA cancer code
> experiments( STAD )
ExperimentList class object of length 13:
[1] STAD_CNASeq-20160128: RaggedExperiment with 31824 rows and 214 columns
[2] STAD_CNASNP-20160128: RaggedExperiment with 443042 rows and 906 columns
[3] STAD_CNVSNP-20160128: RaggedExperiment with 118389 rows and 904 columns
[4] STAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[5] STAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 84 rows and 441 columns
[6] STAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[7] STAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 430 columns
[8] STAD_Mutation-20160128: RaggedExperiment with 148520 rows and 289 columns
[9] STAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 450 columns
[10] STAD_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 36 columns
[11] STAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 357 columns
[12] STAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[13] STAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 397 columns
> rownames( STAD )
CharacterList of length 13
[["STAD_CNASeq-20160128"]] character(0)
[["STAD_CNASNP-20160128"]] character(0)
[["STAD_CNVSNP-20160128"]] character(0)
[["STAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["STAD_GISTIC_Peaks-20160128"]] chr1:10686864-11068052 ...
[["STAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["STAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["STAD_Mutation-20160128"]] character(0)
[["STAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["STAD_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
...
<3 more elements>
> colnames( STAD )
CharacterList of length 13
[["STAD_CNASeq-20160128"]] TCGA-B7-5816-01A-21D-1598-02 ...
[["STAD_CNASNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_CNVSNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_AllByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_Peaks-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_miRNASeqGene-20160128"]] TCGA-3M-AB46-01A-11R-A415-13 ...
[["STAD_Mutation-20160128"]] TCGA-B7-5816-01A-21D-1600-08 ...
[["STAD_RNASeq2GeneNorm-20160128"]] TCGA-3M-AB46-01A-11R-A414-31 ...
[["STAD_RNASeqGene-20160128"]] TCGA-BR-4191-01A-02R-1131-13 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 STAD_CNASeq-20160128 0.9 Mb
2 STAD_CNASNP-20160128 12.1 Mb
3 STAD_CNVSNP-20160128 3.4 Mb
4 STAD_GISTIC_AllByGene-20160128 4.9 Mb
5 STAD_GISTIC_Peaks-20160128 0.1 Mb
6 STAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 STAD_miRNASeqGene-20160128 0.1 Mb
8 STAD_Mutation-20160128 161.5 Mb
9 STAD_RNASeq2GeneNorm-20160128 1.3 Mb
10 STAD_RNASeqGene-20160128 1.7 Mb
11 STAD_RPPAArray-20160128 0 Mb
12 STAD_Methylation_methyl27-20160128 4.9 Mb
13 STAD_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
273 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
170.000 170.000 0.948 0.792 1.085
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 58.00 67.00 65.73 73.00 90.00 9
vital_status:
0 1
268 175
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 194.0 346.0 423.7 553.5 2197.0 273
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 335.5 547.5 673.7 912.0 3720.0 177
tumor_tissue_site:
stomach
443
pathology_M_stage:
m0 m1 mx
391 30 22
gender:
female male
158 285
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2010 2011 2010 2012 2013 6
radiation_therapy:
no yes NA's
323 77 43
residual_tumor:
r0 r1 r2 rx NA's
350 18 19 25 31
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 3.000 5.635 8.000 57.000 51
race:
asian
89
black or african american
13
native hawaiian or other pacific islander
1
white
278
NA's
62
ethnicity:
hispanic or latino not hispanic or latino NA's
5 318 120
Including an additional 1390 columns
A document describing the TCGA cancer code
> experiments( TGCT )
ExperimentList class object of length 10:
[1] TGCT_CNASNP-20160128: RaggedExperiment with 137968 rows and 271 columns
[2] TGCT_CNVSNP-20160128: RaggedExperiment with 25479 rows and 271 columns
[3] TGCT_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[4] TGCT_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 48 rows and 134 columns
[5] TGCT_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[6] TGCT_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 139 columns
[7] TGCT_Mutation-20160128: RaggedExperiment with 14672 rows and 138 columns
[8] TGCT_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 139 columns
[9] TGCT_RPPAArray-20160128: SummarizedExperiment with 192 rows and 107 columns
[10] TGCT_Methylation-20160128: SummarizedExperiment with 485577 rows and 139 columns
> rownames( TGCT )
CharacterList of length 10
[["TGCT_CNASNP-20160128"]] character(0)
[["TGCT_CNVSNP-20160128"]] character(0)
[["TGCT_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["TGCT_GISTIC_Peaks-20160128"]] chr1:1-48649489 ... chr22:18613558-22141824
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["TGCT_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["TGCT_Mutation-20160128"]] character(0)
[["TGCT_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["TGCT_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["TGCT_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( TGCT )
CharacterList of length 10
[["TGCT_CNASNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_CNVSNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_AllByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_Peaks-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_miRNASeqGene-20160128"]] TCGA-2G-AAEW-01A-11R-A439-13 ...
[["TGCT_Mutation-20160128"]] TCGA-2G-AAEW-01A-11D-A42Y-10 ...
[["TGCT_RNASeq2GeneNorm-20160128"]] TCGA-2G-AAEW-01A-11R-A430-07 ...
[["TGCT_RPPAArray-20160128"]] TCGA-2G-AAEW-01A-21-A45P-20 ...
[["TGCT_Methylation-20160128"]] TCGA-2G-AAEW-01A-11D-A42Z-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 TGCT_CNASNP-20160128 3.8 Mb
2 TGCT_CNVSNP-20160128 0.8 Mb
3 TGCT_GISTIC_AllByGene-20160128 4.9 Mb
4 TGCT_GISTIC_Peaks-20160128 0.1 Mb
5 TGCT_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 TGCT_miRNASeqGene-20160128 0.1 Mb
7 TGCT_Mutation-20160128 10 Mb
8 TGCT_RNASeq2GeneNorm-20160128 1.3 Mb
9 TGCT_RPPAArray-20160128 0 Mb
10 TGCT_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
130 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
4.0000 4.0000 1.5493 0.0466 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 26.00 31.00 31.99 37.00 67.00
vital_status:
0 1
130 4
days_to_death:
17 513 618 6972 NA's
1 1 1 1 130
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 688.2 1265.5 2092.7 2826.2 7437.0 4
tumor_tissue_site:
testes
134
pathology_T_stage:
t1 t2 t3 tx
76 51 6 1
pathology_N_stage:
n0 n1 n2 nx NA's
46 11 2 65 10
pathology_M_stage:
m0 m1 m1a m1b NA's
115 2 1 1 15
gender:
male
134
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1992 2006 2009 2008 2012 2013
radiation_therapy:
no yes NA's
111 21 2
karnofsky_performance_score:
80 90 100 NA's
5 41 56 32
race:
asian black or african american white
4 6 119
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
12 111 11
Including an additional 762 columns
A document describing the TCGA cancer code
> experiments( THCA )
ExperimentList class object of length 12:
[1] THCA_CNASeq-20160128: RaggedExperiment with 5953 rows and 203 columns
[2] THCA_CNASNP-20160128: RaggedExperiment with 389998 rows and 1013 columns
[3] THCA_CNVSNP-20160128: RaggedExperiment with 55117 rows and 1013 columns
[4] THCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[5] THCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 38 rows and 499 columns
[6] THCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[7] THCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 569 columns
[8] THCA_Mutation-20160128: RaggedExperiment with 7458 rows and 405 columns
[9] THCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 568 columns
[10] THCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 4 columns
[11] THCA_RPPAArray-20160128: SummarizedExperiment with 175 rows and 224 columns
[12] THCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 567 columns
> rownames( THCA )
CharacterList of length 12
[["THCA_CNASeq-20160128"]] character(0)
[["THCA_CNASNP-20160128"]] character(0)
[["THCA_CNVSNP-20160128"]] character(0)
[["THCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["THCA_GISTIC_Peaks-20160128"]] chr1:158681167-215338621 ...
[["THCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["THCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THCA_Mutation-20160128"]] character(0)
[["THCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["THCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( THCA )
CharacterList of length 12
[["THCA_CNASeq-20160128"]] TCGA-BJ-A0Z2-01A-11D-A10R-02 ...
[["THCA_CNASNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_CNVSNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_AllByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_Peaks-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_miRNASeqGene-20160128"]] TCGA-4C-A93U-01A-11R-A39B-13 ...
[["THCA_Mutation-20160128"]] TCGA-BJ-A0YZ-01A-11D-A10S-08 ...
[["THCA_RNASeq2GeneNorm-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
[["THCA_RNASeqGene-20160128"]] TCGA-DJ-A1QE-01A-21R-A14Y-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 THCA_CNASeq-20160128 0.2 Mb
2 THCA_CNASNP-20160128 10.7 Mb
3 THCA_CNVSNP-20160128 1.8 Mb
4 THCA_GISTIC_AllByGene-20160128 4.9 Mb
5 THCA_GISTIC_Peaks-20160128 0.1 Mb
6 THCA_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 THCA_miRNASeqGene-20160128 0.1 Mb
8 THCA_Mutation-20160128 14 Mb
9 THCA_RNASeq2GeneNorm-20160128 1.3 Mb
10 THCA_RNASeqGene-20160128 1.3 Mb
11 THCA_RPPAArray-20160128 0 Mb
12 THCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
487 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
16.00 16.00 2.80 2.23 4.80
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
15.00 35.00 46.00 47.26 58.00 89.00
vital_status:
0 1
487 16
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
174 743 1021 1176 1631 2973 487
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 535 943 1220 1513 5423 16
tumor_tissue_site:
thyroid
503
pathology_N_stage:
n0 n1 n1a n1b nx
227 58 93 75 50
pathology_M_stage:
m0 m1 mx NA's
280 9 213 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1993 2008 2010 2009 2011 2013
radiation_therapy:
no yes NA's
181 306 16
radiation_exposure:
no yes NA's
423 17 63
extrathyroidal_extension:
minimal (t3) moderate/advanced (t4a) none
133 18 333
very advanced (t4b) NA's
1 18
residual_tumor:
r0 r1 r2 rx NA's
385 52 4 30 32
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 3.658 5.000 41.000 114
multifocality:
multifocal unifocal NA's
227 266 10
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.300 1.700 2.600 2.975 4.000 8.200 100
Including an additional 1481 columns
A document describing the TCGA cancer code
> experiments( THYM )
ExperimentList class object of length 10:
[1] THYM_CNASNP-20160128: RaggedExperiment with 105646 rows and 248 columns
[2] THYM_CNVSNP-20160128: RaggedExperiment with 15571 rows and 248 columns
[3] THYM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[4] THYM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 123 columns
[5] THYM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[6] THYM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 126 columns
[7] THYM_Mutation-20160128: RaggedExperiment with 3064 rows and 123 columns
[8] THYM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 122 columns
[9] THYM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 90 columns
[10] THYM_Methylation-20160128: SummarizedExperiment with 485577 rows and 126 columns
> rownames( THYM )
CharacterList of length 10
[["THYM_CNASNP-20160128"]] character(0)
[["THYM_CNVSNP-20160128"]] character(0)
[["THYM_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["THYM_GISTIC_Peaks-20160128"]] chr1:208606110-249250621 ...
[["THYM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["THYM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THYM_Mutation-20160128"]] character(0)
[["THYM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["THYM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["THYM_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( THYM )
CharacterList of length 10
[["THYM_CNASNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_CNVSNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_AllByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_Peaks-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_miRNASeqGene-20160128"]] TCGA-3G-AB0O-01A-22R-A42W-13 ...
[["THYM_Mutation-20160128"]] TCGA-3G-AB0O-01A-22D-A423-09 ...
[["THYM_RNASeq2GeneNorm-20160128"]] TCGA-3G-AB0O-01A-22R-A42C-07 ...
[["THYM_RPPAArray-20160128"]] TCGA-3G-AB0O-01A-11-A45R-20 ...
[["THYM_Methylation-20160128"]] TCGA-3G-AB0O-01A-22D-A424-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 THYM_CNASNP-20160128 2.9 Mb
2 THYM_CNVSNP-20160128 0.5 Mb
3 THYM_GISTIC_AllByGene-20160128 4.9 Mb
4 THYM_GISTIC_Peaks-20160128 0 Mb
5 THYM_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 THYM_miRNASeqGene-20160128 0.1 Mb
7 THYM_Mutation-20160128 3.3 Mb
8 THYM_RNASeq2GeneNorm-20160128 1.3 Mb
9 THYM_RPPAArray-20160128 0 Mb
10 THYM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
115 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.00 9.00 2.34 1.04 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.00 49.50 60.00 58.15 68.50 84.00 1
vital_status:
0 1
115 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
124 379 853 1423 2488 3488 115
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 725.2 1267.5 1486.3 1947.0 4575.0 10
tumor_tissue_site:
anterior mediastinum thymus
27 97
gender:
female male
60 64
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2008 2010 2010 2012 2013 1
radiation_therapy:
no yes
81 43
race:
asian black or african american white
13 6 103
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
10 100 14
Including an additional 685 columns
A document describing the TCGA cancer code
> experiments( UCEC )
ExperimentList class object of length 14:
[1] UCEC_CNASeq-20160128: RaggedExperiment with 36400 rows and 213 columns
[2] UCEC_CNASNP-20160128: RaggedExperiment with 619412 rows and 1083 columns
[3] UCEC_CNVSNP-20160128: RaggedExperiment with 127094 rows and 1078 columns
[4] UCEC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[5] UCEC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 98 rows and 539 columns
[6] UCEC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[7] UCEC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 433 columns
[8] UCEC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 54 columns
[9] UCEC_Mutation-20160128: RaggedExperiment with 184861 rows and 248 columns
[10] UCEC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 380 columns
[11] UCEC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 269 columns
[12] UCEC_RPPAArray-20160128: SummarizedExperiment with 208 rows and 440 columns
[13] UCEC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 118 columns
[14] UCEC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 466 columns
> rownames( UCEC )
CharacterList of length 14
[["UCEC_CNASeq-20160128"]] character(0)
[["UCEC_CNASNP-20160128"]] character(0)
[["UCEC_CNVSNP-20160128"]] character(0)
[["UCEC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["UCEC_GISTIC_Peaks-20160128"]] chr1:13949775-15575840 ...
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["UCEC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCEC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["UCEC_Mutation-20160128"]] character(0)
[["UCEC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( UCEC )
CharacterList of length 14
[["UCEC_CNASeq-20160128"]] TCGA-A5-A0G5-01A-11D-A043-02 ...
[["UCEC_CNASNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_CNVSNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_AllByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_Peaks-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_miRNASeqGene-20160128"]] TCGA-2E-A9G8-01A-11R-A404-13 ...
[["UCEC_mRNAArray-20160128"]] TCGA-A5-A0G2-01A-11R-A040-07 ...
[["UCEC_Mutation-20160128"]] TCGA-A5-A0G3-01A-11W-A062-09 ...
[["UCEC_RNASeq2GeneNorm-20160128"]] TCGA-A5-A0G1-01A-11R-A118-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UCEC_CNASeq-20160128 1 Mb
2 UCEC_CNASNP-20160128 16.9 Mb
3 UCEC_CNVSNP-20160128 3.7 Mb
4 UCEC_GISTIC_AllByGene-20160128 4.9 Mb
5 UCEC_GISTIC_Peaks-20160128 0.1 Mb
6 UCEC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 UCEC_miRNASeqGene-20160128 0.1 Mb
8 UCEC_mRNAArray-20160128 1.1 Mb
9 UCEC_Mutation-20160128 73.1 Mb
10 UCEC_RNASeq2GeneNorm-20160128 1.3 Mb
11 UCEC_RNASeqGene-20160128 1.3 Mb
12 UCEC_RPPAArray-20160128 0.1 Mb
13 UCEC_Methylation_methyl27-20160128 4.9 Mb
14 UCEC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Available sample meta-data:
---------------------------
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
50.0 367.0 709.0 881.8 1063.0 3423.0 457
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-6.0 543.0 948.5 1195.1 1753.2 6859.0 92
tumor_tissue_site:
endometrial other specify
547 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2007 2009 2009 2010 2013 9
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
145 404 729 1405 2096 4144 535
radiation_therapy:
no yes NA's
295 228 25
histological_type:
endometrioid endometrial adenocarcinoma
411
mixed serous and endometrioid
22
serous endometrial adenocarcinoma
115
residual_tumor:
r0 r1 r2 rx NA's
376 22 16 41 93
Including an additional 1779 columns
A document describing the TCGA cancer code
> experiments( UCS )
ExperimentList class object of length 10:
[1] UCS_CNASNP-20160128: RaggedExperiment with 54944 rows and 111 columns
[2] UCS_CNVSNP-20160128: RaggedExperiment with 19298 rows and 111 columns
[3] UCS_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[4] UCS_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 56 rows and 56 columns
[5] UCS_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[6] UCS_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 56 columns
[7] UCS_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
[8] UCS_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 57 columns
[9] UCS_RPPAArray-20160128: SummarizedExperiment with 192 rows and 48 columns
[10] UCS_Methylation-20160128: SummarizedExperiment with 485577 rows and 57 columns
> rownames( UCS )
CharacterList of length 10
[["UCS_CNASNP-20160128"]] character(0)
[["UCS_CNVSNP-20160128"]] character(0)
[["UCS_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["UCS_GISTIC_Peaks-20160128"]] chr1:1-19401404 ... chr22:41958863-51304566
[["UCS_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["UCS_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCS_Mutation-20160128"]] character(0)
[["UCS_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["UCS_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( UCS )
CharacterList of length 10
[["UCS_CNASNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_CNVSNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_GISTIC_AllByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_Peaks-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_ThresholdedByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_miRNASeqGene-20160128"]] TCGA-N5-A4R8-01A-11R-A28Z-13 ...
[["UCS_Mutation-20160128"]] TCGA-N5-A4R8-01A-11D-A28R-08 ...
[["UCS_RNASeq2GeneNorm-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RPPAArray-20160128"]] TCGA-N5-A4R8-01A-21-A41P-20 ...
[["UCS_Methylation-20160128"]] TCGA-N5-A4R8-01A-11D-A28S-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 UCS_CNASNP-20160128 1.5 Mb
2 UCS_CNVSNP-20160128 0.6 Mb
3 UCS_GISTIC_AllByGene-20160128 4.9 Mb
4 UCS_GISTIC_Peaks-20160128 0.1 Mb
5 UCS_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 UCS_miRNASeqGene-20160128 0.1 Mb
7 UCS_Mutation-20160128 19.7 Mb
8 UCS_RNASeq2GeneNorm-20160128 1.3 Mb
9 UCS_RPPAArray-20160128 0 Mb
10 UCS_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
22 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
35.00 35.00 1.43 1.04 1.96
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
51.00 62.00 68.00 69.72 76.00 90.00
vital_status:
0 1
22 35
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 304.0 522.0 705.4 790.5 3115.0 22
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 591.2 828.0 1183.4 1647.5 4269.0 35
tumor_tissue_site:
uterus
57
gender:
female
57
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2002 2007 2009 2009 2011 2012
radiation_therapy:
no yes NA's
29 25 3
histological_type:
uterine carcinosarcoma/ malignant mixed mullerian tumor (mmmt): nos
24
uterine carcinosarcoma/ mmmt: heterologous type
20
uterine carcinosarcoma/mmmt: homologous type
13
race:
asian black or african american white
3 9 44
NA's
1
ethnicity:
hispanic or latino not hispanic or latino NA's
1 43 13
Including an additional 632 columns
A document describing the TCGA cancer code
> experiments( UVM )
ExperimentList class object of length 11:
[1] UVM_CNASeq-20160128: RaggedExperiment with 6496 rows and 102 columns
[2] UVM_CNASNP-20160128: RaggedExperiment with 69487 rows and 160 columns
[3] UVM_CNVSNP-20160128: RaggedExperiment with 12973 rows and 160 columns
[4] UVM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[5] UVM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 80 columns
[6] UVM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[7] UVM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[8] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
[9] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 80 columns
[10] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns
[11] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( UVM )
CharacterList of length 11
[["UVM_CNASeq-20160128"]] character(0)
[["UVM_CNASNP-20160128"]] character(0)
[["UVM_CNVSNP-20160128"]] character(0)
[["UVM_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["UVM_GISTIC_Peaks-20160128"]] chr1:19073360-24108626 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UVM_Mutation-20160128"]] character(0)
[["UVM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["UVM_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( UVM )
CharacterList of length 11
[["UVM_CNASeq-20160128"]] TCGA-RZ-AB0B-01A-11D-A40D-26 ...
[["UVM_CNASNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_CNVSNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_AllByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_Peaks-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ...
[["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ...
[["UVM_RNASeq2GeneNorm-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
[["UVM_RPPAArray-20160128"]] TCGA-V3-A9ZX-01A-21-A41Z-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 UVM_CNASeq-20160128 0.2 Mb
2 UVM_CNASNP-20160128 1.9 Mb
3 UVM_CNVSNP-20160128 0.4 Mb
4 UVM_GISTIC_AllByGene-20160128 4.9 Mb
5 UVM_GISTIC_Peaks-20160128 0 Mb
6 UVM_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 UVM_miRNASeqGene-20160128 0.1 Mb
8 UVM_Mutation-20160128 12.3 Mb
9 UVM_RNASeq2GeneNorm-20160128 1.3 Mb
10 UVM_RPPAArray-20160128 0 Mb
11 UVM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
23.00 23.00 1.66 1.14 3.05
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
22.00 51.00 61.50 61.65 74.25 86.00
vital_status:
0 1
57 23
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.0 393.5 606.0 693.9 1029.0 1581.0 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 495.0 821.0 861.9 1184.0 2600.0 23
tumor_tissue_site:
choroid
80
pathology_N_stage:
n0 nx NA's
52 27 1
pathology_M_stage:
m0 m1 m1b mx NA's
51 2 2 23 2
gender:
female male
35 45
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2007 2011 2012 2012 2013 2013
radiation_therapy:
no yes NA's
76 3 1
race:
white NA's
55 25
ethnicity:
hispanic or latino not hispanic or latino NA's
1 52 27
Including an additional 448 columns
The curatedTCGAData package provides a convenient and user-friendly interface for The Cancer Genome Atlas data from the Firehose GDAC Pipeline. Please note that _most_ of the data from the GDAC Firehose pipeline uses the 'hg19' reference genome (except for a few cancers; refer to https://confluence.broadinstitute.org/display/GDAC/FAQ).
It is highly recommended to use the 'TCGAutils' companion package. It provides convenience functions for manipulating curatedTCGAData objects. See package for more details (http://bioconductor.org/packages/TCGAutils).
The following are the TCGA disease codes and full names as posted on the official website (https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations).
Study Abbreviation Study Name --------------------------------------------------------------------------- 1 ACC Adrenocortical Carcinoma 2 BLCA Bladder Urothelial Carcinoma 3 BRCA Breast Invasive Carcinoma 4 CESC Cervical Squamous Cell Carcinoma And Endocervical Adenocarcinoma 5 CHOL Cholangiocarcinoma 6 CNTL Controls 7 COAD Colon Adenocarcinoma 8 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 9 ESCA Esophageal Carcinoma 10 GBM Glioblastoma Multiforme 11 HNSC Head And Neck Squamous Cell Carcinoma 12 KICH Kidney Chromophobe 13 KIRC Kidney Renal Clear Cell Carcinoma 14 KIRP Kidney Renal Papillary Cell Carcinoma 15 LAML Acute Myeloid Leukemia 16 LGG Brain Lower Grade Glioma 17 LIHC Liver Hepatocellular Carcinoma 18 LUAD Lung Adenocarcinoma 19 LUSC Lung Squamous Cell Carcinoma 20 MESO Mesothelioma 21 OV Ovarian Serous Cystadenocarcinoma 22 PAAD Pancreatic Adenocarcinoma 23 PCPG Pheochromocytoma And Paraganglioma 24 PRAD Prostate Adenocarcinoma 25 READ Rectum Adenocarcinoma 26 SARC Sarcoma 27 SKCM Skin Cutaneous Melanoma 28 STAD Stomach Adenocarcinoma 29 TGCT Testicular Germ Cell Tumors 30 THCA Thyroid Carcinoma 31 THYM Thymoma 32 UCEC Uterine Corpus Endometrial Carcinoma 33 UCS Uterine Carcinosarcoma 34 UVM Uveal Melanoma
Maintainer: Marcel Ramos [email protected] (ORCID)
Other contributors:
Levi Waldron [email protected] [contributor]
Lucas Schiffer [email protected] [contributor]
Ludwig Geistlinger [email protected] [contributor]
Valerie Obenchain [email protected] [contributor]
Martin Morgan [email protected] [contributor]
Useful links:
Report bugs at https://github.com/waldronlab/curatedTCGAData/issues
help(package = "curatedTCGAData")help(package = "curatedTCGAData")
A document describing the TCGA cancer code
> experiments( ACC )
ExperimentList class object of length 11:
[1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 180 columns
[2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 180 columns
[3] ACC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[4] ACC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 42 rows and 90 columns
[5] ACC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[6] ACC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[7] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
[8] ACC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 79 columns
[9] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 79 columns
[10] ACC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 46 columns
[11] ACC_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] character(0)
[["ACC_CNVSNP-20160128"]] character(0)
[["ACC_GISTIC_AllByGene-20160128"]] character(0)
[["ACC_GISTIC_Peaks-20160128"]] 19 1 20 21 22 2 24 ... 41 42 14 15 16 43 44
[["ACC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ACC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ACC_Mutation-20160128"]] character(0)
[["ACC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_CNVSNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_AllByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_Peaks-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_ThresholdedByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_miRNASeqGene-20160128"]] TCGA-OR-A5J1-01A-11R-A29W-13 ...
[["ACC_Mutation-20160128"]] TCGA-OR-A5J1-01A-11D-A29I-10 ...
[["ACC_RNASeq2Gene-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RNASeq2GeneNorm-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RPPAArray-20160128"]] TCGA-OR-A5J2-01A-21-A39K-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 ACC_CNASNP-20160128 2.2 Mb
2 ACC_CNVSNP-20160128 0.6 Mb
3 ACC_GISTIC_AllByGene-20160128 20.5 Mb
4 ACC_GISTIC_Peaks-20160128 0.1 Mb
5 ACC_GISTIC_ThresholdedByGene-20160128 20.4 Mb
6 ACC_miRNASeqGene-20160128 0.8 Mb
7 ACC_Mutation-20160128 12.6 Mb
8 ACC_RNASeq2Gene-20160128 14.9 Mb
9 ACC_RNASeq2GeneNorm-20160128 14.9 Mb
10 ACC_RPPAArray-20160128 0.1 Mb
11 ACC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
58 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
34.00 34.00 1.51 1.34 3.03
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 35.50 48.50 47.16 60.00 83.00
vital_status:
0 1
58 34
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 399.0 551.5 854.6 1202.2 2405.0 58
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
383.0 917.8 1453.5 1781.6 2339.2 4673.0 34
tumor_tissue_site:
adrenal
92
pathologic_stage:
stage i stage ii stage iii stage iv NA's
9 44 19 18 2
pathology_T_stage:
t1 t2 t3 t4 NA's
9 49 11 21 2
pathology_N_stage:
n0 n1 NA's
80 10 2
gender:
female male
60 32
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1997 2005 2008 2007 2011 2012
radiation_therapy:
no yes NA's
71 18 3
histological_type:
adrenocortical carcinoma- myxoid type
1
adrenocortical carcinoma- oncocytic type
4
adrenocortical carcinoma- usual type
87
residual_tumor:
r0 r1 r2 rx NA's
64 7 12 6 3
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.548 0.500 52.000 61
race:
asian black or african american white
2 1 78
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
8 40 44
Including an additional 806 columns
A document describing the TCGA cancer code
> experiments( ACC )
ExperimentList class object of length 11:
[1] ACC_CNASNP-20160128: RaggedExperiment with 79861 rows and 180 columns
[2] ACC_CNVSNP-20160128: RaggedExperiment with 21052 rows and 180 columns
[3] ACC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[4] ACC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 42 rows and 90 columns
[5] ACC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 90 columns
[6] ACC_Mutation-20160128: RaggedExperiment with 20166 rows and 90 columns
[7] ACC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 79 columns
[8] ACC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 46 columns
[9] ACC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[10] ACC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17716 rows and 79 columns
[11] ACC_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] character(0)
[["ACC_CNVSNP-20160128"]] character(0)
[["ACC_GISTIC_AllByGene-20160128"]] character(0)
[["ACC_GISTIC_Peaks-20160128"]] 19 1 20 21 22 2 24 ... 41 42 14 15 16 43 44
[["ACC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ACC_Mutation-20160128"]] character(0)
[["ACC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ACC_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["ACC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ACC_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( ACC )
CharacterList of length 11
[["ACC_CNASNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_CNVSNP-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_AllByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_Peaks-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_GISTIC_ThresholdedByGene-20160128"]] TCGA-OR-A5J1-01A-11D-A29H-01 ...
[["ACC_Mutation-20160128"]] TCGA-OR-A5J1-01A-11D-A29I-10 ...
[["ACC_RNASeq2Gene-20160128"]] TCGA-OR-A5J1-01A-11R-A29S-07 ...
[["ACC_RPPAArray-20160128"]] TCGA-OR-A5J2-01A-21-A39K-20 ...
[["ACC_miRNASeqGene-20160128"]] TCGA-OR-A5J1-01A-11R-A29W-13 ...
[["ACC_RNASeq2GeneNorm-20160128"]] TCGA-OR-A5J1-01 ... TCGA-PK-A5HB-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 ACC_CNASNP-20160128 2.2 Mb
2 ACC_CNVSNP-20160128 0.6 Mb
3 ACC_GISTIC_AllByGene-20160128 20.5 Mb
4 ACC_GISTIC_Peaks-20160128 0.1 Mb
5 ACC_GISTIC_ThresholdedByGene-20160128 20.4 Mb
6 ACC_Mutation-20160128 12.6 Mb
7 ACC_RNASeq2Gene-20160128 14.9 Mb
8 ACC_RPPAArray-20160128 0.1 Mb
9 ACC_miRNASeqGene-20160128 0.8 Mb
10 ACC_RNASeq2GeneNorm-20160128 12.9 Mb
11 ACC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
58 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 34 34 1.51 1.34 3.03
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 35.50 48.50 47.16 60.00 83.00
vital_status:
0 1
58 34
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 399.0 551.5 854.6 1202.2 2405.0 58
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
383.0 917.8 1453.5 1781.6 2339.2 4673.0 34
tumor_tissue_site:
adrenal
92
pathologic_stage:
stage i stage ii stage iii stage iv NA's
9 44 19 18 2
pathology_T_stage:
t1 t2 t3 t4 NA's
9 49 11 21 2
pathology_N_stage:
n0 n1 NA's
80 10 2
gender:
female male
60 32
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1997 2005 2008 2007 2011 2012
radiation_therapy:
no yes NA's
71 18 3
histological_type:
adrenocortical carcinoma- myxoid type
1
adrenocortical carcinoma- oncocytic type
4
adrenocortical carcinoma- usual type
87
residual_tumor:
r0 r1 r2 rx NA's
64 7 12 6 3
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.548 0.500 52.000 61
race:
asian black or african american white
2 1 78
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
8 40 44
Including an additional 806 columns
A document describing the TCGA cancer code
> experiments( BLCA )
ExperimentList class object of length 13:
[1] BLCA_CNASeq-20160128: RaggedExperiment with 35692 rows and 232 columns
[2] BLCA_CNASNP-20160128: RaggedExperiment with 479978 rows and 806 columns
[3] BLCA_CNVSNP-20160128: RaggedExperiment with 104349 rows and 797 columns
[4] BLCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[5] BLCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 71 rows and 408 columns
[6] BLCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[7] BLCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 429 columns
[8] BLCA_Mutation-20160128: RaggedExperiment with 39312 rows and 130 columns
[9] BLCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 427 columns
[10] BLCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 427 columns
[11] BLCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 67 columns
[12] BLCA_RPPAArray-20160128: SummarizedExperiment with 208 rows and 344 columns
[13] BLCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 434 columns
> rownames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] character(0)
[["BLCA_CNASNP-20160128"]] character(0)
[["BLCA_CNVSNP-20160128"]] character(0)
[["BLCA_GISTIC_AllByGene-20160128"]] character(0)
[["BLCA_GISTIC_Peaks-20160128"]] 38 1 2 3 39 4 40 41 ... 69 70 34 35 36 37 71
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BLCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["BLCA_Mutation-20160128"]] character(0)
[["BLCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] TCGA-BL-A0C8-01A-11D-A10R-02 ...
[["BLCA_CNASNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_CNVSNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_AllByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_Peaks-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_miRNASeqGene-20160128"]] TCGA-2F-A9KO-01A-11R-A38M-13 ...
[["BLCA_Mutation-20160128"]] TCGA-BL-A0C8-01A-11D-A10S-08 ...
[["BLCA_RNASeq2Gene-20160128"]] TCGA-2F-A9KO-01A-11R-A38B-07 ...
[["BLCA_RNASeq2GeneNorm-20160128"]] TCGA-2F-A9KO-01A-11R-A38B-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BLCA_CNASeq-20160128 1 Mb
2 BLCA_CNASNP-20160128 13.1 Mb
3 BLCA_CNVSNP-20160128 3 Mb
4 BLCA_GISTIC_AllByGene-20160128 80.7 Mb
5 BLCA_GISTIC_Peaks-20160128 0.4 Mb
6 BLCA_GISTIC_ThresholdedByGene-20160128 80.5 Mb
7 BLCA_miRNASeqGene-20160128 3.6 Mb
8 BLCA_Mutation-20160128 56.1 Mb
9 BLCA_RNASeq2Gene-20160128 69.4 Mb
10 BLCA_RNASeq2GeneNorm-20160128 69.4 Mb
11 BLCA_RNASeqGene-20160128 13 Mb
12 BLCA_RPPAArray-20160128 0.6 Mb
13 BLCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
232 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
180.000 180.000 1.125 0.992 1.332
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
34.00 60.00 69.00 68.08 76.00 90.00 1
vital_status:
0 1
230 182
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.0 235.8 410.5 552.8 654.5 3183.0 232
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-64.0 398.2 639.0 1016.7 1458.8 5050.0 182
tumor_tissue_site:
bladder
412
pathologic_stage:
stage i stage ii stage iii stage iv NA's
2 131 141 136 2
pathology_M_stage:
m0 m1 mx NA's
196 11 202 3
gender:
female male
108 304
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1999 2009 2011 2010 2012 2013 18
radiation_therapy:
no yes NA's
366 20 26
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 80.00 90.00 83.09 90.00 100.00 276
histological_type:
muscle invasive urothelial carcinoma (pt2 or above)
409
NA's
3
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.00 30.00 39.04 50.00 730.00 188
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.088 2.000 97.000 115
race:
asian black or african american white
44 23 327
NA's
18
ethnicity:
hispanic or latino not hispanic or latino NA's
9 371 32
Including an additional 1695 columns
A document describing the TCGA cancer code
> experiments( BLCA )
ExperimentList class object of length 13:
[1] BLCA_CNASeq-20160128: RaggedExperiment with 35692 rows and 232 columns
[2] BLCA_CNASNP-20160128: RaggedExperiment with 479978 rows and 806 columns
[3] BLCA_CNVSNP-20160128: RaggedExperiment with 104349 rows and 797 columns
[4] BLCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[5] BLCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 71 rows and 408 columns
[6] BLCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[7] BLCA_Mutation-20160128: RaggedExperiment with 39312 rows and 130 columns
[8] BLCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 427 columns
[9] BLCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 67 columns
[10] BLCA_RPPAArray-20160128: SummarizedExperiment with 208 rows and 344 columns
[11] BLCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 429 columns
[12] BLCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18205 rows and 427 columns
[13] BLCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 434 columns
> rownames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] character(0)
[["BLCA_CNASNP-20160128"]] character(0)
[["BLCA_CNVSNP-20160128"]] character(0)
[["BLCA_GISTIC_AllByGene-20160128"]] character(0)
[["BLCA_GISTIC_Peaks-20160128"]] 38 1 2 3 39 4 40 41 ... 69 70 34 35 36 37 71
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BLCA_Mutation-20160128"]] character(0)
[["BLCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] TCGA-BL-A0C8-01A-11D-A10R-02 ...
[["BLCA_CNASNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_CNVSNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_AllByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_Peaks-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_Mutation-20160128"]] TCGA-BL-A0C8-01A-11D-A10S-08 ...
[["BLCA_RNASeq2Gene-20160128"]] TCGA-2F-A9KO-01A-11R-A38B-07 ...
[["BLCA_RNASeqGene-20160128"]] TCGA-BL-A0C8-01A-11R-A10U-07 ...
[["BLCA_RPPAArray-20160128"]] TCGA-2F-A9KO-01A-21-A459-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BLCA_CNASeq-20160128 1 Mb
2 BLCA_CNASNP-20160128 13.1 Mb
3 BLCA_CNVSNP-20160128 3 Mb
4 BLCA_GISTIC_AllByGene-20160128 80.7 Mb
5 BLCA_GISTIC_Peaks-20160128 0.4 Mb
6 BLCA_GISTIC_ThresholdedByGene-20160128 80.5 Mb
7 BLCA_Mutation-20160128 56.1 Mb
8 BLCA_RNASeq2Gene-20160128 69.4 Mb
9 BLCA_RNASeqGene-20160128 13 Mb
10 BLCA_RPPAArray-20160128 0.6 Mb
11 BLCA_miRNASeqGene-20160128 3.6 Mb
12 BLCA_RNASeq2GeneNorm-20160128 61.6 Mb
13 BLCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
232 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 180 180 1.12 0.992 1.33
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
34.00 60.00 69.00 68.08 76.00 90.00 1
vital_status:
0 1
230 182
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.0 235.8 410.5 552.8 654.5 3183.0 232
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-64.0 398.2 639.0 1016.7 1458.8 5050.0 182
tumor_tissue_site:
bladder
412
pathologic_stage:
stage i stage ii stage iii stage iv NA's
2 131 141 136 2
pathology_M_stage:
m0 m1 mx NA's
196 11 202 3
gender:
female male
108 304
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1999 2009 2011 2010 2012 2013 18
radiation_therapy:
no yes NA's
366 20 26
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 80.00 90.00 83.09 90.00 100.00 276
histological_type:
muscle invasive urothelial carcinoma (pt2 or above)
409
NA's
3
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.00 30.00 39.04 50.00 730.00 188
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.088 2.000 97.000 115
race:
asian black or african american white
44 23 327
NA's
18
ethnicity:
hispanic or latino not hispanic or latino NA's
9 371 32
Including an additional 1695 columns
A document describing the TCGA cancer code
> experiments( BRCA )
ExperimentList class object of length 15:
[1] BRCA_CNASeq-20160128: RaggedExperiment with 5298 rows and 38 columns
[2] BRCA_CNASNP-20160128: RaggedExperiment with 1132786 rows and 2209 columns
[3] BRCA_CNVSNP-20160128: RaggedExperiment with 284458 rows and 2199 columns
[4] BRCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[5] BRCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 1080 columns
[6] BRCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[7] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
[8] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
[9] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns
[10] BRCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[11] BRCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[12] BRCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 878 columns
[13] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[14] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
[15] BRCA_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 885 columns
> rownames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] character(0)
[["BRCA_CNASNP-20160128"]] character(0)
[["BRCA_CNVSNP-20160128"]] character(0)
[["BRCA_GISTIC_AllByGene-20160128"]] character(0)
[["BRCA_GISTIC_Peaks-20160128"]] 29 30 1 2 31 3 32 4 ... 66 27 67 28 68 69 70
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BRCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["BRCA_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["BRCA_Mutation-20160128"]] character(0)
[["BRCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<5 more elements>
> colnames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] TCGA-A2-A0EU-01A-22D-A060-02 ...
[["BRCA_CNASNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_CNVSNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_AllByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_Peaks-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_miRNASeqGene-20160128"]] TCGA-3C-AAAU-01A-11R-A41G-13 ...
[["BRCA_mRNAArray-20160128"]] TCGA-A1-A0SD-01A-11R-A115-07 ...
[["BRCA_Mutation-20160128"]] TCGA-A1-A0SB-01A-11D-A142-09 ...
[["BRCA_RNASeq2Gene-20160128"]] TCGA-3C-AAAU-01A-11R-A41B-07 ...
...
<5 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BRCA_CNASeq-20160128 0.2 Mb
2 BRCA_CNASNP-20160128 30.9 Mb
3 BRCA_CNVSNP-20160128 8.2 Mb
4 BRCA_GISTIC_AllByGene-20160128 207.9 Mb
5 BRCA_GISTIC_Peaks-20160128 0.8 Mb
6 BRCA_GISTIC_ThresholdedByGene-20160128 207.7 Mb
7 BRCA_miRNASeqGene-20160128 7.1 Mb
8 BRCA_mRNAArray-20160128 82.5 Mb
9 BRCA_Mutation-20160128 67.4 Mb
10 BRCA_RNASeq2Gene-20160128 192.3 Mb
11 BRCA_RNASeq2GeneNorm-20160128 192.3 Mb
12 BRCA_RNASeqGene-20160128 140 Mb
13 BRCA_RPPAArray-20160128 1.8 Mb
14 BRCA_Methylation_methyl27-20160128 4.9 Mb
15 BRCA_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
947 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
151.00 151.00 3.48 2.83 4.50
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.0 49.0 59.0 58.6 68.0 90.0 16
vital_status:
0 1 NA's
945 152 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
116.0 700.5 1272.0 1644.7 2367.0 7455.0 947
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-7 440 761 1183 1572 8605 153
tumor_tissue_site:
breast NA's
1097 1
pathology_M_stage:
cm0 (i+) m0 m1 mx NA's
6 906 22 163 1
gender:
female male NA's
1085 12 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1988 2007 2009 2008 2010 2013 3
days_to_last_known_alive:
735 2576 NA's
1 1 1096
radiation_therapy:
no yes NA's
446 556 96
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.363 2.000 35.000 169
race:
american indian or alaska native asian
1 61
black or african american white
183 757
NA's
96
ethnicity:
hispanic or latino not hispanic or latino NA's
39 884 175
Including an additional 2667 columns
A document describing the TCGA cancer code
> experiments( BRCA )
ExperimentList class object of length 15:
[1] BRCA_CNASeq-20160128: RaggedExperiment with 5298 rows and 38 columns
[2] BRCA_CNASNP-20160128: RaggedExperiment with 1132786 rows and 2209 columns
[3] BRCA_CNVSNP-20160128: RaggedExperiment with 284458 rows and 2199 columns
[4] BRCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[5] BRCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 1080 columns
[6] BRCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[7] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
[8] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns
[9] BRCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[10] BRCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 878 columns
[11] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[12] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
[13] BRCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18300 rows and 1212 columns
[14] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
[15] BRCA_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 885 columns
> rownames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] character(0)
[["BRCA_CNASNP-20160128"]] character(0)
[["BRCA_CNVSNP-20160128"]] character(0)
[["BRCA_GISTIC_AllByGene-20160128"]] character(0)
[["BRCA_GISTIC_Peaks-20160128"]] 29 30 1 2 31 3 32 4 ... 66 27 67 28 68 69 70
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BRCA_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["BRCA_Mutation-20160128"]] character(0)
[["BRCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BRCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<5 more elements>
> colnames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] TCGA-A2-A0EU-01A-22D-A060-02 ...
[["BRCA_CNASNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_CNVSNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_AllByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_Peaks-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_mRNAArray-20160128"]] TCGA-A1-A0SD-01A-11R-A115-07 ...
[["BRCA_Mutation-20160128"]] TCGA-A1-A0SB-01A-11D-A142-09 ...
[["BRCA_RNASeq2Gene-20160128"]] TCGA-3C-AAAU-01A-11R-A41B-07 ...
[["BRCA_RNASeqGene-20160128"]] TCGA-A1-A0SB-01A-11R-A144-07 ...
...
<5 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BRCA_CNASeq-20160128 0.2 Mb
2 BRCA_CNASNP-20160128 30.9 Mb
3 BRCA_CNVSNP-20160128 8.2 Mb
4 BRCA_GISTIC_AllByGene-20160128 207.9 Mb
5 BRCA_GISTIC_Peaks-20160128 0.8 Mb
6 BRCA_GISTIC_ThresholdedByGene-20160128 207.7 Mb
7 BRCA_mRNAArray-20160128 82.5 Mb
8 BRCA_Mutation-20160128 67.4 Mb
9 BRCA_RNASeq2Gene-20160128 192.3 Mb
10 BRCA_RNASeqGene-20160128 140 Mb
11 BRCA_RPPAArray-20160128 1.8 Mb
12 BRCA_miRNASeqGene-20160128 7.1 Mb
13 BRCA_RNASeq2GeneNorm-20160128 171.7 Mb
14 BRCA_Methylation_methyl27-20160128 4.9 Mb
15 BRCA_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
947 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 151 151 3.48 2.83 4.5
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.0 49.0 59.0 58.6 68.0 90.0 16
vital_status:
0 1 NA's
945 152 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
116.0 700.5 1272.0 1644.7 2367.0 7455.0 947
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-7 440 761 1183 1572 8605 153
tumor_tissue_site:
breast NA's
1097 1
pathology_M_stage:
cm0 (i+) m0 m1 mx NA's
6 906 22 163 1
gender:
female male NA's
1085 12 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1988 2007 2009 2008 2010 2013 3
days_to_last_known_alive:
735 2576 NA's
1 1 1096
radiation_therapy:
no yes NA's
446 556 96
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.363 2.000 35.000 169
race:
american indian or alaska native asian
1 61
black or african american white
183 757
NA's
96
ethnicity:
hispanic or latino not hispanic or latino NA's
39 884 175
Including an additional 2667 columns
A document describing the TCGA cancer code
> experiments( CESC )
ExperimentList class object of length 12:
[1] CESC_CNASeq-20160128: RaggedExperiment with 7834 rows and 100 columns
[2] CESC_CNASNP-20160128: RaggedExperiment with 267855 rows and 586 columns
[3] CESC_CNVSNP-20160128: RaggedExperiment with 59450 rows and 586 columns
[4] CESC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[5] CESC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 60 rows and 295 columns
[6] CESC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[7] CESC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 312 columns
[8] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
[9] CESC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 309 columns
[10] CESC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 309 columns
[11] CESC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 173 columns
[12] CESC_Methylation-20160128: SummarizedExperiment with 485577 rows and 312 columns
> rownames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] character(0)
[["CESC_CNASNP-20160128"]] character(0)
[["CESC_CNVSNP-20160128"]] character(0)
[["CESC_GISTIC_AllByGene-20160128"]] character(0)
[["CESC_GISTIC_Peaks-20160128"]] 27 1 28 2 3 29 4 30 ... 23 58 59 24 60 25 61
[["CESC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CESC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CESC_Mutation-20160128"]] character(0)
[["CESC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CESC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] TCGA-C5-A1BQ-01C-11D-A20X-26 ...
[["CESC_CNASNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_CNVSNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_AllByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_Peaks-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_miRNASeqGene-20160128"]] TCGA-2W-A8YY-01A-11R-A37P-13 ...
[["CESC_Mutation-20160128"]] TCGA-BI-A0VR-01A-11D-A10S-08 ...
[["CESC_RNASeq2Gene-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
[["CESC_RNASeq2GeneNorm-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 CESC_CNASeq-20160128 0.3 Mb
2 CESC_CNASNP-20160128 7.3 Mb
3 CESC_CNVSNP-20160128 1.8 Mb
4 CESC_GISTIC_AllByGene-20160128 59.3 Mb
5 CESC_GISTIC_Peaks-20160128 0.3 Mb
6 CESC_GISTIC_ThresholdedByGene-20160128 59.1 Mb
7 CESC_miRNASeqGene-20160128 2.7 Mb
8 CESC_Mutation-20160128 32.9 Mb
9 CESC_RNASeq2Gene-20160128 50.9 Mb
10 CESC_RNASeq2GeneNorm-20160128 50.9 Mb
11 CESC_RPPAArray-20160128 0.3 Mb
12 CESC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
235 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
72.00 72.00 1.70 1.39 2.29
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 38.0 46.0 48.2 56.0 88.0 2
vital_status:
0 1
235 72
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 349.5 620.0 881.3 1069.5 4086.0 235
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 374 688 1071 1362 6408 72
tumor_tissue_site:
cervical
307
pathology_N_stage:
n0 n1 nx NA's
135 60 67 45
pathology_M_stage:
m0 m1 mx NA's
116 10 131 50
gender:
female
307
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
radiation_therapy:
no yes NA's
55 129 123
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
ethnicity:
hispanic or latino not hispanic or latino NA's
24 171 112
weight_kg_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.25 70.50 73.04 83.75 210.00 29
tumor_status:
tumor free with tumor NA's
201 80 26
tobacco_smoking_year_stopped:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1995 2003 2000 2010 2013 264
tobacco_smoking_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
tobacco_smoking_history:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 1.000 1.829 2.000 5.000 44
agebegansmokinginyears:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.00 16.00 18.00 21.14 24.00 44.00 222
radiation_therapy_status:
completed as planned treatment not completed NA's
29 3 275
pregnancies_count_total:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 2.00 3.00 3.61 5.00 15.00 40
pregnancies_count_stillbirth:
0 1 3 NA's
106 5 1 195
pregnancy_spontaneous_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.5442 1.0000 6.0000 160
pregnancies_count_live_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.250 2.000 2.844 4.000 11.000 45
pregnancy_therapeutic_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.8525 1.0000 13.0000 185
pregnancies_count_ectopic:
0 1 2 NA's
104 11 1 191
lymph_node_location:
lymph_node_location_positive_pathology_name|lymph_node_location_positive_pathology_text
307
menopause_status:
indeterminate (neither pre or postmenopausal)
3
peri (6-12 months since last menstrual period)
25
post (prior bilateral ovariectomy or >12 mo since lmp with no prior hysterectomy)
84
pre (<6 months since lmp and no prior bilateral ovariectomy and not on estrogen replacement)
125
NA's
70
lymphovascular_involvement:
absent present NA's
72 80 155
lymph_nodes_examined_he_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
lymph_nodes_examined:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.00 13.00 21.00 22.28 29.00 63.00 127
keratinization_squamous_cell:
keratinizing squamous cell carcinoma
55
non-keratinizing squamous cell carcinoma
120
NA's
132
initial_pathologic_dx_year:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
hysterectomy_type:
hysterectomy_performed_type|hysterectomy_performed_text
307
history_hormonal_contraceptives_use:
current user former user never used NA's
15 54 90 148
height_cm_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
132 157 160 161 165 183 43
corpus_involvement:
absent present NA's
99 19 189
chemo_concurrent_type:
carboplatin cisplatin other NA's
7 104 2 194
cervix_suv_results:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 8.70 12.00 13.22 16.92 28.80 290
cause_of_death:
cardiopulmonary arrest lung cancer renal failure
1 1 1
NA's
304
age_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
20.00 38.00 46.00 48.27 56.50 88.00
Including an additional 1330 columns
A document describing the TCGA cancer code
> experiments( CESC )
ExperimentList class object of length 12:
[1] CESC_CNASeq-20160128: RaggedExperiment with 7834 rows and 100 columns
[2] CESC_CNASNP-20160128: RaggedExperiment with 267855 rows and 586 columns
[3] CESC_CNVSNP-20160128: RaggedExperiment with 59450 rows and 586 columns
[4] CESC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[5] CESC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 60 rows and 295 columns
[6] CESC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 295 columns
[7] CESC_Mutation-20160128: RaggedExperiment with 46547 rows and 194 columns
[8] CESC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 309 columns
[9] CESC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 173 columns
[10] CESC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 312 columns
[11] CESC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18162 rows and 309 columns
[12] CESC_Methylation-20160128: SummarizedExperiment with 485577 rows and 312 columns
> rownames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] character(0)
[["CESC_CNASNP-20160128"]] character(0)
[["CESC_CNVSNP-20160128"]] character(0)
[["CESC_GISTIC_AllByGene-20160128"]] character(0)
[["CESC_GISTIC_Peaks-20160128"]] 27 1 28 2 3 29 4 30 ... 23 58 59 24 60 25 61
[["CESC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CESC_Mutation-20160128"]] character(0)
[["CESC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CESC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CESC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( CESC )
CharacterList of length 12
[["CESC_CNASeq-20160128"]] TCGA-C5-A1BQ-01C-11D-A20X-26 ...
[["CESC_CNASNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_CNVSNP-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_AllByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_Peaks-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2W-A8YY-01A-11D-A37M-01 ...
[["CESC_Mutation-20160128"]] TCGA-BI-A0VR-01A-11D-A10S-08 ...
[["CESC_RNASeq2Gene-20160128"]] TCGA-2W-A8YY-01A-11R-A37O-07 ...
[["CESC_RPPAArray-20160128"]] TCGA-2W-A8YY-01A-21-A40H-20 ...
[["CESC_miRNASeqGene-20160128"]] TCGA-2W-A8YY-01A-11R-A37P-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 CESC_CNASeq-20160128 0.3 Mb
2 CESC_CNASNP-20160128 7.3 Mb
3 CESC_CNVSNP-20160128 1.8 Mb
4 CESC_GISTIC_AllByGene-20160128 59.3 Mb
5 CESC_GISTIC_Peaks-20160128 0.3 Mb
6 CESC_GISTIC_ThresholdedByGene-20160128 59.1 Mb
7 CESC_Mutation-20160128 32.9 Mb
8 CESC_RNASeq2Gene-20160128 50.9 Mb
9 CESC_RPPAArray-20160128 0.3 Mb
10 CESC_miRNASeqGene-20160128 2.7 Mb
11 CESC_RNASeq2GeneNorm-20160128 45.1 Mb
12 CESC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
235 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 72 72 1.7 1.39 2.29
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 38.0 46.0 48.2 56.0 88.0 2
vital_status:
0 1
235 72
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 349.5 620.0 881.3 1069.5 4086.0 235
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 374 688 1071 1362 6408 72
tumor_tissue_site:
cervical
307
pathology_N_stage:
n0 n1 nx NA's
135 60 67 45
pathology_M_stage:
m0 m1 mx NA's
116 10 131 50
gender:
female
307
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
radiation_therapy:
no yes NA's
55 129 123
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
ethnicity:
hispanic or latino not hispanic or latino NA's
24 171 112
weight_kg_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.25 70.50 73.04 83.75 210.00 29
tumor_status:
tumor free with tumor NA's
201 80 26
tobacco_smoking_year_stopped:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1995 2003 2000 2010 2013 264
tobacco_smoking_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.20 6.50 15.00 17.38 25.00 57.00 214
tobacco_smoking_history:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.000 1.000 1.000 1.829 2.000 5.000 44
agebegansmokinginyears:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.00 16.00 18.00 21.14 24.00 44.00 222
radiation_therapy_status:
completed as planned treatment not completed NA's
29 3 275
pregnancies_count_total:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 2.00 3.00 3.61 5.00 15.00 40
pregnancies_count_stillbirth:
0 1 3 NA's
106 5 1 195
pregnancy_spontaneous_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.5442 1.0000 6.0000 160
pregnancies_count_live_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.250 2.000 2.844 4.000 11.000 45
pregnancy_therapeutic_abortion_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.8525 1.0000 13.0000 185
pregnancies_count_ectopic:
0 1 2 NA's
104 11 1 191
lymph_node_location:
lymph_node_location_positive_pathology_name|lymph_node_location_positive_pathology_text
307
menopause_status:
indeterminate (neither pre or postmenopausal)
3
peri (6-12 months since last menstrual period)
25
post (prior bilateral ovariectomy or >12 mo since lmp with no prior hysterectomy)
84
pre (<6 months since lmp and no prior bilateral ovariectomy and not on estrogen replacement)
125
NA's
70
lymphovascular_involvement:
absent present NA's
72 80 155
lymph_nodes_examined_he_count:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 1.044 1.000 16.000 148
lymph_nodes_examined:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.00 13.00 21.00 22.28 29.00 63.00 127
keratinization_squamous_cell:
keratinizing squamous cell carcinoma
55
non-keratinizing squamous cell carcinoma
120
NA's
132
initial_pathologic_dx_year:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2006 2010 2008 2012 2013 2
hysterectomy_type:
hysterectomy_performed_type|hysterectomy_performed_text
307
history_hormonal_contraceptives_use:
current user former user never used NA's
15 54 90 148
height_cm_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
132 157 160 161 165 183 43
corpus_involvement:
absent present NA's
99 19 189
chemo_concurrent_type:
carboplatin cisplatin other NA's
7 104 2 194
cervix_suv_results:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 8.70 12.00 13.22 16.92 28.80 290
cause_of_death:
cardiopulmonary arrest lung cancer renal failure
1 1 1
NA's
304
age_at_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
20.00 38.00 46.00 48.27 56.50 88.00
Including an additional 1330 columns
A document describing the TCGA cancer code
> experiments( CHOL )
ExperimentList class object of length 11:
[1] CHOL_CNASNP-20160128: RaggedExperiment with 39698 rows and 85 columns
[2] CHOL_CNVSNP-20160128: RaggedExperiment with 7570 rows and 85 columns
[3] CHOL_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[4] CHOL_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 19 rows and 36 columns
[5] CHOL_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[6] CHOL_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 45 columns
[7] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns
[8] CHOL_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 45 columns
[9] CHOL_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 45 columns
[10] CHOL_RPPAArray-20160128: SummarizedExperiment with 192 rows and 30 columns
[11] CHOL_Methylation-20160128: SummarizedExperiment with 485577 rows and 45 columns
> rownames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] character(0)
[["CHOL_CNVSNP-20160128"]] character(0)
[["CHOL_GISTIC_AllByGene-20160128"]] character(0)
[["CHOL_GISTIC_Peaks-20160128"]] 4 1 5 6 7 8 9 10 ... 13 3 14 15 18 16 17 20
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CHOL_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CHOL_Mutation-20160128"]] character(0)
[["CHOL_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CHOL_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["CHOL_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_CNVSNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_AllByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_Peaks-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_miRNASeqGene-20160128"]] TCGA-3X-AAV9-01A-72R-A41D-13 ...
[["CHOL_Mutation-20160128"]] TCGA-3X-AAV9-01A-72D-A417-09 ...
[["CHOL_RNASeq2Gene-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ...
[["CHOL_RNASeq2GeneNorm-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ...
[["CHOL_RPPAArray-20160128"]] TCGA-3X-AAV9-01A-81-A45N-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 CHOL_CNASNP-20160128 1.1 Mb
2 CHOL_CNVSNP-20160128 0.2 Mb
3 CHOL_GISTIC_AllByGene-20160128 10.2 Mb
4 CHOL_GISTIC_Peaks-20160128 0 Mb
5 CHOL_GISTIC_ThresholdedByGene-20160128 10.1 Mb
6 CHOL_miRNASeqGene-20160128 0.5 Mb
7 CHOL_Mutation-20160128 4.6 Mb
8 CHOL_RNASeq2Gene-20160128 9.6 Mb
9 CHOL_RNASeq2GeneNorm-20160128 9.6 Mb
10 CHOL_RPPAArray-20160128 0.1 Mb
11 CHOL_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
18 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
18.000 18.000 1.370 0.742 2.532
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 56.50 66.50 63.03 72.00 82.00
vital_status:
0 1
18 18
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
21.0 195.2 500.0 592.9 731.0 1939.0 18
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.0 539.8 942.5 936.6 1394.0 1976.0 18
tumor_tissue_site:
bile duct
36
pathology_T_stage:
t1 t2 t2a t2b t3
19 6 2 4 5
pathology_N_stage:
n0 n1 nx
26 5 5
pathology_M_stage:
m0 m1 mx
28 5 3
gender:
female male
20 16
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2005 2010 2011 2010 2012 2013
radiation_therapy:
no NA's
35 1
histological_type:
cholangiocarcinoma; distal cholangiocarcinoma; hilar/perihilar
2 4
cholangiocarcinoma; intrahepatic
30
residual_tumor:
r0 r1 rx
28 5 3
race:
asian black or african american white
3 2 31
ethnicity:
hispanic or latino not hispanic or latino NA's
2 33 1
Including an additional 622 columns
A document describing the TCGA cancer code
> experiments( CHOL )
ExperimentList class object of length 11:
[1] CHOL_CNASNP-20160128: RaggedExperiment with 39698 rows and 85 columns
[2] CHOL_CNVSNP-20160128: RaggedExperiment with 7570 rows and 85 columns
[3] CHOL_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[4] CHOL_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 19 rows and 36 columns
[5] CHOL_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns
[6] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns
[7] CHOL_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 45 columns
[8] CHOL_RPPAArray-20160128: SummarizedExperiment with 192 rows and 30 columns
[9] CHOL_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 45 columns
[10] CHOL_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18002 rows and 45 columns
[11] CHOL_Methylation-20160128: SummarizedExperiment with 485577 rows and 45 columns
> rownames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] character(0)
[["CHOL_CNVSNP-20160128"]] character(0)
[["CHOL_GISTIC_AllByGene-20160128"]] character(0)
[["CHOL_GISTIC_Peaks-20160128"]] 4 1 5 6 7 8 9 10 ... 13 3 14 15 18 16 17 20
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["CHOL_Mutation-20160128"]] character(0)
[["CHOL_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["CHOL_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["CHOL_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["CHOL_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<1 more element>
> colnames( CHOL )
CharacterList of length 11
[["CHOL_CNASNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_CNVSNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_AllByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_Peaks-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_GISTIC_ThresholdedByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ...
[["CHOL_Mutation-20160128"]] TCGA-3X-AAV9-01A-72D-A417-09 ...
[["CHOL_RNASeq2Gene-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ...
[["CHOL_RPPAArray-20160128"]] TCGA-3X-AAV9-01A-81-A45N-20 ...
[["CHOL_miRNASeqGene-20160128"]] TCGA-3X-AAV9-01A-72R-A41D-13 ...
[["CHOL_RNASeq2GeneNorm-20160128"]] TCGA-3X-AAV9-01 ... TCGA-ZU-A8S4-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 CHOL_CNASNP-20160128 1.1 Mb
2 CHOL_CNVSNP-20160128 0.2 Mb
3 CHOL_GISTIC_AllByGene-20160128 10.2 Mb
4 CHOL_GISTIC_Peaks-20160128 0 Mb
5 CHOL_GISTIC_ThresholdedByGene-20160128 10.1 Mb
6 CHOL_Mutation-20160128 4.6 Mb
7 CHOL_RNASeq2Gene-20160128 9.6 Mb
8 CHOL_RPPAArray-20160128 0.1 Mb
9 CHOL_miRNASeqGene-20160128 0.5 Mb
10 CHOL_RNASeq2GeneNorm-20160128 8.4 Mb
11 CHOL_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
18 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 18 18 1.37 0.742 2.53
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
29.00 56.50 66.50 63.03 72.00 82.00
vital_status:
0 1
18 18
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
21.0 195.2 500.0 592.9 731.0 1939.0 18
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.0 539.8 942.5 936.6 1394.0 1976.0 18
tumor_tissue_site:
bile duct
36
pathology_T_stage:
t1 t2 t2a t2b t3
19 6 2 4 5
pathology_N_stage:
n0 n1 nx
26 5 5
pathology_M_stage:
m0 m1 mx
28 5 3
gender:
female male
20 16
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2005 2010 2011 2010 2012 2013
radiation_therapy:
no NA's
35 1
histological_type:
cholangiocarcinoma; distal cholangiocarcinoma; hilar/perihilar
2 4
cholangiocarcinoma; intrahepatic
30
residual_tumor:
r0 r1 rx
28 5 3
race:
asian black or african american white
3 2 31
ethnicity:
hispanic or latino not hispanic or latino NA's
2 33 1
Including an additional 622 columns
A document describing the TCGA cancer code
> experiments( COAD )
ExperimentList class object of length 16:
[1] COAD_CNASeq-20160128: RaggedExperiment with 40530 rows and 136 columns
[2] COAD_CNASNP-20160128: RaggedExperiment with 459490 rows and 914 columns
[3] COAD_CNVSNP-20160128: RaggedExperiment with 90534 rows and 914 columns
[4] COAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[5] COAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 66 rows and 449 columns
[6] COAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[7] COAD_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 221 columns
[8] COAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 172 columns
[9] COAD_Mutation-20160128: RaggedExperiment with 62530 rows and 154 columns
[10] COAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 326 columns
[11] COAD_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 191 columns
[12] COAD_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 326 columns
[13] COAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 10 columns
[14] COAD_RPPAArray-20160128: SummarizedExperiment with 208 rows and 360 columns
[15] COAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 202 columns
[16] COAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 333 columns
> rownames( COAD )
CharacterList of length 16
[["COAD_CNASeq-20160128"]] character(0)
[["COAD_CNASNP-20160128"]] character(0)
[["COAD_CNVSNP-20160128"]] character(0)
[["COAD_GISTIC_AllByGene-20160128"]] character(0)
[["COAD_GISTIC_Peaks-20160128"]] 23 24 25 26 27 1 28 ... 18 19 20 21 22 65 66
[["COAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["COAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["COAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["COAD_Mutation-20160128"]] character(0)
[["COAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<6 more elements>
> colnames( COAD )
CharacterList of length 16
[["COAD_CNASeq-20160128"]] TCGA-A6-2671-01A-01D-1405-02 ...
[["COAD_CNASNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_CNVSNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_AllByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_Peaks-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_miRNASeqGene-20160128"]] TCGA-A6-2675-01A-02T-1722-13 ...
[["COAD_mRNAArray-20160128"]] TCGA-A6-2671-11A-01R-1758-07 ...
[["COAD_Mutation-20160128"]] TCGA-A6-2672-01A-01W-0833-10 ...
[["COAD_RNASeq2Gene-20160128"]] TCGA-3L-AA1B-01A-11R-A37K-07 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 COAD_CNASeq-20160128 1.1 Mb
2 COAD_CNASNP-20160128 12.5 Mb
3 COAD_CNVSNP-20160128 2.7 Mb
4 COAD_GISTIC_AllByGene-20160128 88.5 Mb
5 COAD_GISTIC_Peaks-20160128 0.4 Mb
6 COAD_GISTIC_ThresholdedByGene-20160128 88.3 Mb
7 COAD_miRNASeqGene-20160128 1.3 Mb
8 COAD_mRNAArray-20160128 25.6 Mb
9 COAD_Mutation-20160128 23.6 Mb
10 COAD_RNASeq2Gene-20160128 53.6 Mb
11 COAD_RNASeq2GeneNorm_illuminaga-20160128 32.5 Mb
12 COAD_RNASeq2GeneNorm_illuminahiseq-20160128 53.6 Mb
13 COAD_RNASeqGene-20160128 4.1 Mb
14 COAD_RPPAArray-20160128 0.7 Mb
15 COAD_Methylation_methyl27-20160128 4.9 Mb
16 COAD_Methylation_methyl450-20160128 75 Mb
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.00 68.00 66.95 77.00 90.00 2
tumor_tissue_site:
colon NA's
456 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2007 2009 2008 2010 2013
radiation_therapy:
no yes NA's
378 9 70
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.058 2.000 50.000 25
race:
american indian or alaska native asian
1 11
black or african american white
59 213
NA's
173
ethnicity:
hispanic or latino not hispanic or latino NA's
4 270 183
Including an additional 2604 columns
A document describing the TCGA cancer code
> experiments( COAD )
ExperimentList class object of length 17:
[1] COAD_CNASeq-20160128: RaggedExperiment with 40530 rows and 136 columns
[2] COAD_CNASNP-20160128: RaggedExperiment with 459490 rows and 914 columns
[3] COAD_CNVSNP-20160128: RaggedExperiment with 90534 rows and 914 columns
[4] COAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[5] COAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 66 rows and 449 columns
[6] COAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[7] COAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 172 columns
[8] COAD_Mutation-20160128: RaggedExperiment with 62530 rows and 154 columns
[9] COAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 326 columns
[10] COAD_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 191 columns
[11] COAD_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 326 columns
[12] COAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 10 columns
[13] COAD_RPPAArray-20160128: SummarizedExperiment with 208 rows and 360 columns
[14] COAD_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 221 columns
[15] COAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18025 rows and 498 columns
[16] COAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 202 columns
[17] COAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 333 columns
> rownames( COAD )
CharacterList of length 17
[["COAD_CNASeq-20160128"]] character(0)
[["COAD_CNASNP-20160128"]] character(0)
[["COAD_CNVSNP-20160128"]] character(0)
[["COAD_GISTIC_AllByGene-20160128"]] character(0)
[["COAD_GISTIC_Peaks-20160128"]] 23 24 25 26 27 1 28 ... 18 19 20 21 22 65 66
[["COAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["COAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["COAD_Mutation-20160128"]] character(0)
[["COAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["COAD_RNASeq2GeneNorm_illuminaga-20160128"]] A1BG A1CF ... psiTPTE22 tAKR
...
<7 more elements>
> colnames( COAD )
CharacterList of length 17
[["COAD_CNASeq-20160128"]] TCGA-A6-2671-01A-01D-1405-02 ...
[["COAD_CNASNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_CNVSNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_AllByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_Peaks-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_mRNAArray-20160128"]] TCGA-A6-2671-11A-01R-1758-07 ...
[["COAD_Mutation-20160128"]] TCGA-A6-2672-01A-01W-0833-10 ...
[["COAD_RNASeq2Gene-20160128"]] TCGA-3L-AA1B-01A-11R-A37K-07 ...
[["COAD_RNASeq2GeneNorm_illuminaga-20160128"]] TCGA-A6-2671-01A-01R-1410-07...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 COAD_CNASeq-20160128 1.1 Mb
2 COAD_CNASNP-20160128 12.5 Mb
3 COAD_CNVSNP-20160128 2.7 Mb
4 COAD_GISTIC_AllByGene-20160128 88.5 Mb
5 COAD_GISTIC_Peaks-20160128 0.4 Mb
6 COAD_GISTIC_ThresholdedByGene-20160128 88.3 Mb
7 COAD_mRNAArray-20160128 25.6 Mb
8 COAD_Mutation-20160128 23.6 Mb
9 COAD_RNASeq2Gene-20160128 53.6 Mb
10 COAD_RNASeq2GeneNorm_illuminaga-20160128 32.5 Mb
11 COAD_RNASeq2GeneNorm_illuminahiseq-20160128 53.6 Mb
12 COAD_RNASeqGene-20160128 4.1 Mb
13 COAD_RPPAArray-20160128 0.7 Mb
14 COAD_miRNASeqGene-20160128 1.3 Mb
15 COAD_RNASeq2GeneNorm-20160128 70.8 Mb
16 COAD_Methylation_methyl27-20160128 4.9 Mb
17 COAD_Methylation_methyl450-20160128 75 Mb
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.00 68.00 66.95 77.00 90.00 2
tumor_tissue_site:
colon NA's
456 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2007 2009 2008 2010 2013
radiation_therapy:
no yes NA's
378 9 70
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.058 2.000 50.000 25
race:
american indian or alaska native asian
1 11
black or african american white
59 213
NA's
173
ethnicity:
hispanic or latino not hispanic or latino NA's
4 270 183
Including an additional 2604 columns
curatedTCGAData assembles data on-the-fly from ExperimentHub
to provide cohesive MultiAssayExperiment container objects.
All the user has to do is to provide TCGA disease code(s) and assay types.
It is highly recommended to use the companion package TCGAutils,
developed to work with TCGA data specifically from curatedTCGAData and
some flat files.
curatedTCGAData( diseaseCode = "*", assays = "*", version, dry.run = TRUE, verbose = TRUE, ... )curatedTCGAData( diseaseCode = "*", assays = "*", version, dry.run = TRUE, verbose = TRUE, ... )
diseaseCode |
character() A vector of TCGA cancer cohort codes
(e.g., |
assays |
character() A vector of TCGA assays, glob matches allowed; see below for more details |
version |
character(1) One of |
dry.run |
logical(1) Whether to return the dataset names before actual download (default TRUE) |
verbose |
logical(1) Whether to show the dataset currenlty being (down)loaded (default TRUE) |
... |
Additional arguments passed on to the
|
This function will check against available resources in
ExperimentHub. Only the latest runDate ("2016-01-28") is supported.
Use the dry.run = FALSE to download remote datasets and
build an integrative MultiAssayExperiment object.
For a list of 'diseaseCodes', see the curatedTCGAData-package
help page.
a MultiAssayExperiment of the specified assays and
cancer codes or informative data.frame of resources when dry.run is TRUE
Below is a list of partial ExperimentList assay names and their respective
description. These assays can be entered as part of the assays
argument in the main function. Partial glob matches are allowed such as:
'CN*' for "CNASeq", "CNASNP", "CNVSNP" assays. Credit: Ludwig G.
ExperimentList data types Description
----------------------------------------------------------------------------
SummarizedExperiment*
RNASeqGene Gene expression values
RNASeq2Gene RSEM TPM gene expression values
RNASeq2GeneNorm Upper quartile log2 normalized RSEM TPM gene
expression values
miRNAArray Probe-level miRNA expression values
miRNASeqGene Gene-level log2 RPM miRNA expression values
mRNAArray Unified gene-level mRNA expression values
mRNAArray_huex Gene-level mRNA expression values from Affymetrix
Human Exon Array
mRNAArray_TX_g4502a Gene-level mRNA expression values from Agilent
244K Array
mRNAArray_TX_ht_hg_u133a Gene-level mRNA expression values from Affymetrix
Human Genome U133 Array
GISTIC_AllByGene Gene-level GISTIC2 copy number values
GISTIC_ThresholdedByGene Gene-level GISTIC2 thresholded discrete copy
number values
RPPAArray Reverse Phase Protein Array normalized protein
expression values
RangedSummarizedExperiment
GISTIC_Peaks GISTIC2 thresholded discrete copy number values
in recurrent peak regions
SummarizedExperiment with HDF5Array DelayedMatrix
Methylation_methyl27 Probe-level methylation beta values from Illumina
HumanMethylation 27K BeadChip
Methylation_methyl450 Probe-level methylation beta values from Infinium
HumanMethylation 450K BeadChip
RaggedExperiment
CNASNP Segmented somatic Copy Number Alteration calls
from SNP array
CNVSNP Segmented germline Copy Number Variant calls from
SNP Array
CNASeq Segmented somatic Copy Number Alteration calls
from low pass DNA Sequencing
Mutation* Somatic mutations calls
CNACGH_CGH_hg_244a Segmented somatic Copy Number Alteration calls
from CGH Agilent Microarray 244A
CNACGH_CGH_hg_415k_g4124a Segmented somatic Copy Number Alteration calls
from CGH Agilent Microarray 415K
* All can be converted to RangedSummarizedExperiment (except RPPAArray) with
TCGAutils
Version 2.1.1 provides a couple of corrections to the colData for ovarian
cancer (OV) and skin cancer (SKCM). In these new data, the cancer
subtype variables are fully available. One get obtain the mapping of columns
to subtypes in the colData with the getSubtypeMap function in
TCGAutils.
Version 2.1.0 provides gene-level log2 RPM miRNA expression values for
miRNASeqGene data log2 normalized RSEM for RNASeq2GeneNorm assays.
Previously, the data provided were read counts and normalized counts,
respectively. See issue #53 on GitHub for
additional details.
The new version 2.0.1 includes various improvements including an
additional assay that provides RNASeq2Gene data as RSEM TPM gene
expression values (issue #38). Additional changes include genomic
information for RaggedExperiment type data objects where '37' is now
'GRCh37' as reported in issue #40. Datasets (e.g., OV, GBM) that contain
multiple assays that could be merged are now provided as merged assays
(issue #27). We corrected an issue where mRNAArray assays were returning
DataFrames instead of matrix type data (issue #31). Version 1.1.38
provides the original run of curatedTCGAData and is provided due to legacy
reasons.
curatedTCGAData-package
curatedTCGAData( diseaseCode = c("GBM", "ACC"), assays = "CNASNP", version = "2.0.1" ) curatedTCGAData("BRCA", "GISTIC*", "2.0.1")curatedTCGAData( diseaseCode = c("GBM", "ACC"), assays = "CNASNP", version = "2.0.1" ) curatedTCGAData("BRCA", "GISTIC*", "2.0.1")
A document describing the TCGA cancer code
> experiments( DLBC )
ExperimentList class object of length 11:
[1] DLBC_CNASNP-20160128: RaggedExperiment with 44725 rows and 94 columns
[2] DLBC_CNVSNP-20160128: RaggedExperiment with 9343 rows and 94 columns
[3] DLBC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[4] DLBC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 39 rows and 48 columns
[5] DLBC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[6] DLBC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 47 columns
[7] DLBC_Mutation-20160128: RaggedExperiment with 16918 rows and 48 columns
[8] DLBC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 48 columns
[9] DLBC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 48 columns
[10] DLBC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 33 columns
[11] DLBC_Methylation-20160128: SummarizedExperiment with 485577 rows and 48 columns
> rownames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] character(0)
[["DLBC_CNVSNP-20160128"]] character(0)
[["DLBC_GISTIC_AllByGene-20160128"]] character(0)
[["DLBC_GISTIC_Peaks-20160128"]] 15 17 16 1 2 18 19 ... 36 37 12 38 39 13 40
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["DLBC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["DLBC_Mutation-20160128"]] character(0)
[["DLBC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["DLBC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["DLBC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_CNVSNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_AllByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_Peaks-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_miRNASeqGene-20160128"]] TCGA-FA-8693-01A-11R-2401-13 ...
[["DLBC_Mutation-20160128"]] TCGA-FA-8693-01A-11D-2397-10 ...
[["DLBC_RNASeq2Gene-20160128"]] TCGA-FA-8693-01A-11R-2404-07 ...
[["DLBC_RNASeq2GeneNorm-20160128"]] TCGA-FA-8693-01A-11R-2404-07 ...
[["DLBC_RPPAArray-20160128"]] TCGA-FA-8693-01A-21-A45K-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 DLBC_CNASNP-20160128 1.2 Mb
2 DLBC_CNVSNP-20160128 0.3 Mb
3 DLBC_GISTIC_AllByGene-20160128 12.5 Mb
4 DLBC_GISTIC_Peaks-20160128 0.1 Mb
5 DLBC_GISTIC_ThresholdedByGene-20160128 12.4 Mb
6 DLBC_miRNASeqGene-20160128 0.5 Mb
7 DLBC_Mutation-20160128 12.6 Mb
8 DLBC_RNASeq2Gene-20160128 10.1 Mb
9 DLBC_RNASeq2GeneNorm-20160128 10.1 Mb
10 DLBC_RPPAArray-20160128 0.1 Mb
11 DLBC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
39 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.000 9.000 1.630 0.858 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
23.00 46.00 57.50 56.27 67.00 82.00
vital_status:
0 1
39 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
58 313 595 1505 1252 6425 39
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 616 946 1328 1581 5980 9
gender:
female male
26 22
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1987 2009 2011 2009 2012 2013
radiation_therapy:
no yes NA's
40 7 1
histological_type:
diffuse large b-cell lymphoma (dlbcl) nos (any anatomic site nodal or extranodal)
41
primary dlbcl of the cns
3
primary mediastinal (thymic) dlbcl
4
race:
asian black or african american white
18 1 29
ethnicity:
hispanic or latino not hispanic or latino
12 36
Including an additional 607 columns
A document describing the TCGA cancer code
> experiments( DLBC )
ExperimentList class object of length 11:
[1] DLBC_CNASNP-20160128: RaggedExperiment with 44725 rows and 94 columns
[2] DLBC_CNVSNP-20160128: RaggedExperiment with 9343 rows and 94 columns
[3] DLBC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[4] DLBC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 39 rows and 48 columns
[5] DLBC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 48 columns
[6] DLBC_Mutation-20160128: RaggedExperiment with 16918 rows and 48 columns
[7] DLBC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 48 columns
[8] DLBC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 33 columns
[9] DLBC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 47 columns
[10] DLBC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17665 rows and 48 columns
[11] DLBC_Methylation-20160128: SummarizedExperiment with 485577 rows and 48 columns
> rownames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] character(0)
[["DLBC_CNVSNP-20160128"]] character(0)
[["DLBC_GISTIC_AllByGene-20160128"]] character(0)
[["DLBC_GISTIC_Peaks-20160128"]] 15 17 16 1 2 18 19 ... 36 37 12 38 39 13 40
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["DLBC_Mutation-20160128"]] character(0)
[["DLBC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["DLBC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["DLBC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["DLBC_RNASeq2GeneNorm-20160128"]] A1BG A2LD1 A2ML1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( DLBC )
CharacterList of length 11
[["DLBC_CNASNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_CNVSNP-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_AllByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_Peaks-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_GISTIC_ThresholdedByGene-20160128"]] TCGA-FA-8693-01A-11D-2389-01 ...
[["DLBC_Mutation-20160128"]] TCGA-FA-8693-01A-11D-2397-10 ...
[["DLBC_RNASeq2Gene-20160128"]] TCGA-FA-8693-01A-11R-2404-07 ...
[["DLBC_RPPAArray-20160128"]] TCGA-FA-8693-01A-21-A45K-20 ...
[["DLBC_miRNASeqGene-20160128"]] TCGA-FA-8693-01A-11R-2401-13 ...
[["DLBC_RNASeq2GeneNorm-20160128"]] TCGA-FA-8693-01 ... TCGA-VB-A8QN-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 DLBC_CNASNP-20160128 1.2 Mb
2 DLBC_CNVSNP-20160128 0.3 Mb
3 DLBC_GISTIC_AllByGene-20160128 12.5 Mb
4 DLBC_GISTIC_Peaks-20160128 0.1 Mb
5 DLBC_GISTIC_ThresholdedByGene-20160128 12.4 Mb
6 DLBC_Mutation-20160128 12.6 Mb
7 DLBC_RNASeq2Gene-20160128 10.1 Mb
8 DLBC_RPPAArray-20160128 0.1 Mb
9 DLBC_miRNASeqGene-20160128 0.5 Mb
10 DLBC_RNASeq2GeneNorm-20160128 8.7 Mb
11 DLBC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
39 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 9 9 1.63 0.858 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
23.00 46.00 57.50 56.27 67.00 82.00
vital_status:
0 1
39 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
58 313 595 1505 1252 6425 39
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 616 946 1328 1581 5980 9
gender:
female male
26 22
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1987 2009 2011 2009 2012 2013
radiation_therapy:
no yes NA's
40 7 1
histological_type:
diffuse large b-cell lymphoma (dlbcl) nos (any anatomic site nodal or extranodal)
41
primary dlbcl of the cns
3
primary mediastinal (thymic) dlbcl
4
race:
asian black or african american white
18 1 29
ethnicity:
hispanic or latino not hispanic or latino
12 36
Including an additional 607 columns
A document describing the TCGA cancer code
> experiments( ESCA )
ExperimentList class object of length 13:
[1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns
[2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns
[3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns
[4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns
[6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[7] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns
[8] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
[9] ESCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 196 columns
[10] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 196 columns
[11] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns
[12] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns
[13] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns
> rownames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] character(0)
[["ESCA_CNASNP-20160128"]] character(0)
[["ESCA_CNVSNP-20160128"]] character(0)
[["ESCA_GISTIC_AllByGene-20160128"]] character(0)
[["ESCA_GISTIC_Peaks-20160128"]] 31 1 32 2 3 33 4 34 ... 73 74 29 75 76 77 78
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ESCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ESCA_Mutation-20160128"]] character(0)
[["ESCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ESCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ...
[["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_miRNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37J-13 ...
[["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ...
[["ESCA_RNASeq2Gene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RNASeq2GeneNorm-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 ESCA_CNASeq-20160128 0.5 Mb
2 ESCA_CNASNP-20160128 5.5 Mb
3 ESCA_CNVSNP-20160128 1.7 Mb
4 ESCA_GISTIC_AllByGene-20160128 38.3 Mb
5 ESCA_GISTIC_Peaks-20160128 0.2 Mb
6 ESCA_GISTIC_ThresholdedByGene-20160128 38.1 Mb
7 ESCA_miRNASeqGene-20160128 1.8 Mb
8 ESCA_Mutation-20160128 45 Mb
9 ESCA_RNASeq2Gene-20160128 33.2 Mb
10 ESCA_RNASeq2GeneNorm-20160128 33.2 Mb
11 ESCA_RNASeqGene-20160128 42.8 Mb
12 ESCA_RPPAArray-20160128 0.2 Mb
13 ESCA_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
108 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
77.000 77.000 0.962 0.677 1.353
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 54.00 61.00 62.46 72.00 90.00
vital_status:
0 1
108 77
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 180.0 351.0 495.2 650.0 2532.0 108
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 336.5 402.5 570.1 696.8 3714.0 77
tumor_tissue_site:
esophagus
185
pathology_M_stage:
m0 m1 m1a mx NA's
136 4 5 18 22
gender:
female male
27 158
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1998 2007 2011 2009 2012 2013 7
radiation_therapy:
no yes NA's
124 43 18
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 60.00 80.00 73.82 90.00 100.00 117
histological_type:
esophagus adenocarcinoma, nos esophagus squamous cell carcinoma
89 96
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 17.62 30.00 34.48 47.25 102.00 87
residual_tumor:
r0 r1 r2 rx NA's
137 13 2 7 26
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.526 4.000 21.000 50
race:
asian black or african american white
46 5 114
NA's
20
ethnicity:
hispanic or latino not hispanic or latino NA's
6 88 91
Including an additional 940 columns
A document describing the TCGA cancer code
> experiments( ESCA )
ExperimentList class object of length 13:
[1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns
[2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns
[3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns
[4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns
[6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[7] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
[8] ESCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 196 columns
[9] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns
[10] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns
[11] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns
[12] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18730 rows and 196 columns
[13] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns
> rownames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] character(0)
[["ESCA_CNASNP-20160128"]] character(0)
[["ESCA_CNVSNP-20160128"]] character(0)
[["ESCA_GISTIC_AllByGene-20160128"]] character(0)
[["ESCA_GISTIC_Peaks-20160128"]] 31 1 32 2 3 33 4 34 ... 73 74 29 75 76 77 78
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["ESCA_Mutation-20160128"]] character(0)
[["ESCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["ESCA_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
[["ESCA_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( ESCA )
CharacterList of length 13
[["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ...
[["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ...
[["ESCA_RNASeq2Gene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RPPAArray-20160128"]] TCGA-2H-A9GF-01A-21-A41Y-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 ESCA_CNASeq-20160128 0.5 Mb
2 ESCA_CNASNP-20160128 5.5 Mb
3 ESCA_CNVSNP-20160128 1.7 Mb
4 ESCA_GISTIC_AllByGene-20160128 38.3 Mb
5 ESCA_GISTIC_Peaks-20160128 0.2 Mb
6 ESCA_GISTIC_ThresholdedByGene-20160128 38.1 Mb
7 ESCA_Mutation-20160128 45 Mb
8 ESCA_RNASeq2Gene-20160128 33.2 Mb
9 ESCA_RNASeqGene-20160128 42.8 Mb
10 ESCA_RPPAArray-20160128 0.2 Mb
11 ESCA_miRNASeqGene-20160128 1.8 Mb
12 ESCA_RNASeq2GeneNorm-20160128 30.4 Mb
13 ESCA_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
108 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 77 77 0.962 0.677 1.35
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 54.00 61.00 62.46 72.00 90.00
vital_status:
0 1
108 77
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 180.0 351.0 495.2 650.0 2532.0 108
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 336.5 402.5 570.1 696.8 3714.0 77
tumor_tissue_site:
esophagus
185
pathology_M_stage:
m0 m1 m1a mx NA's
136 4 5 18 22
gender:
female male
27 158
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1998 2007 2011 2009 2012 2013 7
radiation_therapy:
no yes NA's
124 43 18
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 60.00 80.00 73.82 90.00 100.00 117
histological_type:
esophagus adenocarcinoma, nos esophagus squamous cell carcinoma
89 96
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 17.62 30.00 34.48 47.25 102.00 87
residual_tumor:
r0 r1 r2 rx NA's
137 13 2 7 26
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.526 4.000 21.000 50
race:
asian black or african american white
46 5 114
NA's
20
ethnicity:
hispanic or latino not hispanic or latino NA's
6 88 91
Including an additional 940 columns
A document describing the TCGA cancer code
> experiments( GBM )
ExperimentList class object of length 18:
[1] GBM_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 81512 rows and 438 columns
[2] GBM_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 57975 rows and 338 columns
[3] GBM_CNASNP-20160128: RaggedExperiment with 602338 rows and 1104 columns
[4] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
[5] GBM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[6] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
[7] GBM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[8] GBM_miRNAArray-20160128: SummarizedExperiment with 534 rows and 565 columns
[9] GBM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 0 columns
[10] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns
[11] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 502 columns
[12] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns
[13] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns
[14] GBM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 166 columns
[15] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns
[16] GBM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 244 columns
[17] GBM_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 285 columns
[18] GBM_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 154 columns
> rownames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["GBM_CNASNP-20160128"]] character(0)
[["GBM_CNVSNP-20160128"]] character(0)
[["GBM_GISTIC_AllByGene-20160128"]] character(0)
[["GBM_GISTIC_Peaks-20160128"]] 25 26 1 27 28 2 29 3 ... 65 22 23 66 67 24 68
[["GBM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["GBM_miRNAArray-20160128"]] ebv-miR-BART1-3p ... kshv-miR-K12-9*
[["GBM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["GBM_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
...
<8 more elements>
> colnames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] TCGA-02-0001-01C-01D-0185-02 ...
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-02-2466-01A-01D-0787-02 ...
[["GBM_CNASNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_CNVSNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_AllByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_Peaks-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_ThresholdedByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_miRNAArray-20160128"]] TCGA-02-0001-01C-01T-0179-07 ...
[["GBM_miRNASeqGene-20160128"]] character(0)
[["GBM_mRNAArray_huex-20160128"]] TCGA-02-0001-01C-01R-0178-03 ...
...
<8 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 GBM_CNACGH_CGH_hg_244a-20160128 2.3 Mb
2 GBM_CNACGH_CGH_hg_415k_g4124a-20160128 1.7 Mb
3 GBM_CNASNP-20160128 16.4 Mb
4 GBM_CNVSNP-20160128 4.2 Mb
5 GBM_GISTIC_AllByGene-20160128 112.7 Mb
6 GBM_GISTIC_Peaks-20160128 0.5 Mb
7 GBM_GISTIC_ThresholdedByGene-20160128 112.5 Mb
8 GBM_miRNAArray-20160128 2.5 Mb
9 GBM_miRNASeqGene-20160128 0.2 Mb
10 GBM_mRNAArray_huex-20160128 63.7 Mb
11 GBM_mRNAArray_TX_g4502a-20160128 70.5 Mb
12 GBM_mRNAArray_TX_ht_hg_u133a-20160128 50.1 Mb
13 GBM_Mutation-20160128 31 Mb
14 GBM_RNASeq2Gene-20160128 28.5 Mb
15 GBM_RNASeq2GeneNorm-20160128 28.5 Mb
16 GBM_RPPAArray-20160128 0.5 Mb
17 GBM_Methylation_methyl27-20160128 4.9 Mb
18 GBM_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
109 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
490.000 490.000 1.047 0.981 1.156
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.00 50.00 59.00 57.82 68.00 89.00 4
vital_status:
0 1 NA's
104 491 4
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 170.5 382.0 504.5 609.2 3881.0 109
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 156.2 261.0 479.4 628.0 2818.0 497
tumor_tissue_site:
brain NA's
595 4
gender:
female male NA's
230 365 4
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1989 2002 2006 2005 2009 2013 4
radiation_therapy:
no yes NA's
78 489 32
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 70.00 80.00 77.04 80.00 100.00 157
histological_type:
glioblastoma multiforme (gbm) treated primary gbm
31 20
untreated primary (de novo) gbm NA's
544 4
race:
asian black or african american white
13 51 506
NA's
29
ethnicity:
hispanic or latino not hispanic or latino NA's
13 489 97
Including an additional 4368 columns
A document describing the TCGA cancer code
> experiments( GBM )
ExperimentList class object of length 18:
[1] GBM_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 81512 rows and 438 columns
[2] GBM_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 57975 rows and 338 columns
[3] GBM_CNASNP-20160128: RaggedExperiment with 602338 rows and 1104 columns
[4] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns
[5] GBM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[6] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns
[7] GBM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns
[8] GBM_miRNAArray-20160128: SummarizedExperiment with 534 rows and 565 columns
[9] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns
[10] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 502 columns
[11] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns
[12] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns
[13] GBM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 166 columns
[14] GBM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 244 columns
[15] GBM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 0 columns
[16] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18199 rows and 166 columns
[17] GBM_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 285 columns
[18] GBM_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 154 columns
> rownames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["GBM_CNASNP-20160128"]] character(0)
[["GBM_CNVSNP-20160128"]] character(0)
[["GBM_GISTIC_AllByGene-20160128"]] character(0)
[["GBM_GISTIC_Peaks-20160128"]] 25 26 1 27 28 2 29 3 ... 65 22 23 66 67 24 68
[["GBM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["GBM_miRNAArray-20160128"]] ebv-miR-BART1-3p ... kshv-miR-K12-9*
[["GBM_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["GBM_mRNAArray_TX_g4502a-20160128"]] 15E1.2 2'-PDE ... tcag7.23 tcag7.350
...
<8 more elements>
> colnames( GBM )
CharacterList of length 18
[["GBM_CNACGH_CGH_hg_244a-20160128"]] TCGA-02-0001-01C-01D-0185-02 ...
[["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-02-2466-01A-01D-0787-02 ...
[["GBM_CNASNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_CNVSNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_AllByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_Peaks-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_GISTIC_ThresholdedByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ...
[["GBM_miRNAArray-20160128"]] TCGA-02-0001-01C-01T-0179-07 ...
[["GBM_mRNAArray_huex-20160128"]] TCGA-02-0001-01C-01R-0178-03 ...
[["GBM_mRNAArray_TX_g4502a-20160128"]] TCGA-02-0001-01C-01R-0179-07 ...
...
<8 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 GBM_CNACGH_CGH_hg_244a-20160128 2.3 Mb
2 GBM_CNACGH_CGH_hg_415k_g4124a-20160128 1.7 Mb
3 GBM_CNASNP-20160128 16.4 Mb
4 GBM_CNVSNP-20160128 4.2 Mb
5 GBM_GISTIC_AllByGene-20160128 112.7 Mb
6 GBM_GISTIC_Peaks-20160128 0.5 Mb
7 GBM_GISTIC_ThresholdedByGene-20160128 112.5 Mb
8 GBM_miRNAArray-20160128 2.5 Mb
9 GBM_mRNAArray_huex-20160128 63.7 Mb
10 GBM_mRNAArray_TX_g4502a-20160128 70.5 Mb
11 GBM_mRNAArray_TX_ht_hg_u133a-20160128 50.1 Mb
12 GBM_Mutation-20160128 31 Mb
13 GBM_RNASeq2Gene-20160128 28.5 Mb
14 GBM_RPPAArray-20160128 0.5 Mb
15 GBM_miRNASeqGene-20160128 0.2 Mb
16 GBM_RNASeq2GeneNorm-20160128 25.3 Mb
17 GBM_Methylation_methyl27-20160128 4.9 Mb
18 GBM_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
109 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 490 490 1.05 0.981 1.16
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
10.00 50.00 59.00 57.82 68.00 89.00 4
vital_status:
0 1 NA's
104 491 4
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 170.5 382.0 504.5 609.2 3881.0 109
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 156.2 261.0 479.4 628.0 2818.0 497
tumor_tissue_site:
brain NA's
595 4
gender:
female male NA's
230 365 4
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1989 2002 2006 2005 2009 2013 4
radiation_therapy:
no yes NA's
78 489 32
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 70.00 80.00 77.04 80.00 100.00 157
histological_type:
glioblastoma multiforme (gbm) treated primary gbm
31 20
untreated primary (de novo) gbm NA's
544 4
race:
asian black or african american white
13 51 506
NA's
29
ethnicity:
hispanic or latino not hispanic or latino NA's
13 489 97
Including an additional 4368 columns
A document describing the TCGA cancer code
> experiments( HNSC )
ExperimentList class object of length 13:
[1] HNSC_CNASeq-20160128: RaggedExperiment with 32905 rows and 225 columns
[2] HNSC_CNASNP-20160128: RaggedExperiment with 499142 rows and 1090 columns
[3] HNSC_CNVSNP-20160128: RaggedExperiment with 110289 rows and 1089 columns
[4] HNSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[5] HNSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 72 rows and 522 columns
[6] HNSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[7] HNSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
[8] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
[9] HNSC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 566 columns
[10] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 566 columns
[11] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
[12] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
[13] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns
> rownames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] character(0)
[["HNSC_GISTIC_Peaks-20160128"]] 29 30 31 1 32 33 2 ... 25 26 70 71 72 27 73
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["HNSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] TCGA-BA-4074-01A-01D-1431-02 ...
[["HNSC_CNASNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_CNVSNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_AllByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_Peaks-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_miRNASeqGene-20160128"]] TCGA-4P-AA8J-01A-11R-A39B-13 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2Gene-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeq2GeneNorm-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 HNSC_CNASeq-20160128 1 Mb
2 HNSC_CNASNP-20160128 13.6 Mb
3 HNSC_CNVSNP-20160128 3.3 Mb
4 HNSC_GISTIC_AllByGene-20160128 102.3 Mb
5 HNSC_GISTIC_Peaks-20160128 0.5 Mb
6 HNSC_GISTIC_ThresholdedByGene-20160128 102.1 Mb
7 HNSC_miRNASeqGene-20160128 4.5 Mb
8 HNSC_Mutation-20160128 68.9 Mb
9 HNSC_RNASeq2Gene-20160128 91.2 Mb
10 HNSC_RNASeq2GeneNorm-20160128 91.2 Mb
11 HNSC_RNASeqGene-20160128 48.6 Mb
12 HNSC_RPPAArray-20160128 0.3 Mb
13 HNSC_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
305 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
223.00 223.00 1.18 1.06 1.35
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.00 53.00 61.00 60.91 69.00 89.00 1
vital_status:
0 1
304 224
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 260.0 430.0 740.0 814.5 6417.0 305
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.0 529.5 851.0 1042.9 1404.0 5480.0 225
tumor_tissue_site:
head and neck
528
pathology_M_stage:
m0 m1 mx NA's
191 1 65 271
gender:
female male
142 386
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2007 2010 2008 2011 2013 1
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
98.0 483.0 848.5 1226.9 1647.5 3930.0 506
radiation_therapy:
no yes NA's
163 303 62
histological_type:
head & neck squamous cell carcinoma
517
head & neck squamous cell carcinoma basaloid type
10
head & neck squamous cell carcinoma, spindle cell variant
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.01685 25.00000 40.00000 45.75496 60.00000 300.00000 230
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1936 1959 1968 1967 1975 2001 246
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.186 3.000 44.000 115
race:
american indian or alaska native asian
2 11
black or african american white
48 452
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
26 465 37
Including an additional 1426 columns
A document describing the TCGA cancer code
> experiments( HNSC )
ExperimentList class object of length 13:
[1] HNSC_CNASeq-20160128: RaggedExperiment with 32905 rows and 225 columns
[2] HNSC_CNASNP-20160128: RaggedExperiment with 499142 rows and 1090 columns
[3] HNSC_CNVSNP-20160128: RaggedExperiment with 110289 rows and 1089 columns
[4] HNSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[5] HNSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 72 rows and 522 columns
[6] HNSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 522 columns
[7] HNSC_Mutation-20160128: RaggedExperiment with 51799 rows and 279 columns
[8] HNSC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 566 columns
[9] HNSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 294 columns
[10] HNSC_RPPAArray-20160128: SummarizedExperiment with 160 rows and 212 columns
[11] HNSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 532 columns
[12] HNSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18361 rows and 566 columns
[13] HNSC_Methylation-20160128: SummarizedExperiment with 485577 rows and 580 columns
> rownames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] character(0)
[["HNSC_CNASNP-20160128"]] character(0)
[["HNSC_CNVSNP-20160128"]] character(0)
[["HNSC_GISTIC_AllByGene-20160128"]] character(0)
[["HNSC_GISTIC_Peaks-20160128"]] 29 30 31 1 32 33 2 ... 25 26 70 71 72 27 73
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["HNSC_Mutation-20160128"]] character(0)
[["HNSC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["HNSC_RPPAArray-20160128"]] 14-3-3_epsilon 4E-BP1 ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( HNSC )
CharacterList of length 13
[["HNSC_CNASeq-20160128"]] TCGA-BA-4074-01A-01D-1431-02 ...
[["HNSC_CNASNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_CNVSNP-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_AllByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_Peaks-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-4P-AA8J-01A-11D-A390-01 ...
[["HNSC_Mutation-20160128"]] TCGA-BA-4074-01A-01D-1434-08 ...
[["HNSC_RNASeq2Gene-20160128"]] TCGA-4P-AA8J-01A-11R-A39I-07 ...
[["HNSC_RNASeqGene-20160128"]] TCGA-BA-4074-01A-01R-1436-07 ...
[["HNSC_RPPAArray-20160128"]] TCGA-BA-4074-01A-21-2072-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 HNSC_CNASeq-20160128 1 Mb
2 HNSC_CNASNP-20160128 13.6 Mb
3 HNSC_CNVSNP-20160128 3.3 Mb
4 HNSC_GISTIC_AllByGene-20160128 102.3 Mb
5 HNSC_GISTIC_Peaks-20160128 0.5 Mb
6 HNSC_GISTIC_ThresholdedByGene-20160128 102.1 Mb
7 HNSC_Mutation-20160128 68.9 Mb
8 HNSC_RNASeq2Gene-20160128 91.2 Mb
9 HNSC_RNASeqGene-20160128 48.6 Mb
10 HNSC_RPPAArray-20160128 0.3 Mb
11 HNSC_miRNASeqGene-20160128 4.5 Mb
12 HNSC_RNASeq2GeneNorm-20160128 81.6 Mb
13 HNSC_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
305 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 223 223 1.18 1.06 1.35
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.00 53.00 61.00 60.91 69.00 89.00 1
vital_status:
0 1
304 224
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 260.0 430.0 740.0 814.5 6417.0 305
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
11.0 529.5 851.0 1042.9 1404.0 5480.0 225
tumor_tissue_site:
head and neck
528
pathology_M_stage:
m0 m1 mx NA's
191 1 65 271
gender:
female male
142 386
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2007 2010 2008 2011 2013 1
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
98.0 483.0 848.5 1226.9 1647.5 3930.0 506
radiation_therapy:
no yes NA's
163 303 62
histological_type:
head & neck squamous cell carcinoma
517
head & neck squamous cell carcinoma basaloid type
10
head & neck squamous cell carcinoma, spindle cell variant
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.01685 25.00000 40.00000 45.75496 60.00000 300.00000 230
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1936 1959 1968 1967 1975 2001 246
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.186 3.000 44.000 115
race:
american indian or alaska native asian
2 11
black or african american white
48 452
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
26 465 37
Including an additional 1426 columns
A document describing the TCGA cancer code
> experiments( KICH )
ExperimentList class object of length 11:
[1] KICH_CNASNP-20160128: RaggedExperiment with 57729 rows and 132 columns
[2] KICH_CNVSNP-20160128: RaggedExperiment with 10164 rows and 132 columns
[3] KICH_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[4] KICH_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 2 rows and 66 columns
[5] KICH_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[6] KICH_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 91 columns
[7] KICH_Mutation-20160128: RaggedExperiment with 7559 rows and 66 columns
[8] KICH_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 91 columns
[9] KICH_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 91 columns
[10] KICH_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[11] KICH_Methylation-20160128: SummarizedExperiment with 485577 rows and 66 columns
> rownames( KICH )
CharacterList of length 11
[["KICH_CNASNP-20160128"]] character(0)
[["KICH_CNVSNP-20160128"]] character(0)
[["KICH_GISTIC_AllByGene-20160128"]] character(0)
[["KICH_GISTIC_Peaks-20160128"]] 1 2
[["KICH_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KICH_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KICH_Mutation-20160128"]] character(0)
[["KICH_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KICH_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["KICH_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( KICH )
CharacterList of length 11
[["KICH_CNASNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_CNVSNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_AllByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_Peaks-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_ThresholdedByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_miRNASeqGene-20160128"]] TCGA-KL-8323-01A-21R-2314-13 ...
[["KICH_Mutation-20160128"]] TCGA-KL-8323-01A-21D-2310-10 ...
[["KICH_RNASeq2Gene-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ...
[["KICH_RNASeq2GeneNorm-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ...
[["KICH_RPPAArray-20160128"]] TCGA-KL-8324-01A-21-A421-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 KICH_CNASNP-20160128 1.6 Mb
2 KICH_CNVSNP-20160128 0.3 Mb
3 KICH_GISTIC_AllByGene-20160128 15.9 Mb
4 KICH_GISTIC_Peaks-20160128 0 Mb
5 KICH_GISTIC_ThresholdedByGene-20160128 15.8 Mb
6 KICH_miRNASeqGene-20160128 0.9 Mb
7 KICH_Mutation-20160128 2.6 Mb
8 KICH_RNASeq2Gene-20160128 16.8 Mb
9 KICH_RNASeq2GeneNorm-20160128 16.8 Mb
10 KICH_RPPAArray-20160128 0.1 Mb
11 KICH_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.00 9.00 2.34 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
17.00 42.00 50.00 51.52 61.75 86.00
vital_status:
0 1
56 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
325 725 855 1001 1158 2172 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 1366 2713 2320 3138 4676 10
tumor_tissue_site:
kidney
66
pathologic_stage:
stage i stage ii stage iii stage iv
21 25 14 6
pathology_N_stage:
n0 n1 n2 nx
40 3 2 21
pathology_M_stage:
m0 m1 mx NA's
34 2 9 21
gender:
female male
27 39
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2000 2004 2005 2005 2007 2011
radiation_therapy:
no
66
karnofsky_performance_score:
90 100 NA's
3 10 53
histological_type:
kidney chromophobe
66
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 8.00 24.00 25.09 31.00 75.00 55
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1964 1974 1974 1984 1997 58
race:
asian black or african american white
2 4 58
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
4 32 30
Including an additional 718 columns
A document describing the TCGA cancer code
> experiments( KICH )
ExperimentList class object of length 11:
[1] KICH_CNASNP-20160128: RaggedExperiment with 57729 rows and 132 columns
[2] KICH_CNVSNP-20160128: RaggedExperiment with 10164 rows and 132 columns
[3] KICH_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[4] KICH_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 2 rows and 66 columns
[5] KICH_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns
[6] KICH_Mutation-20160128: RaggedExperiment with 7559 rows and 66 columns
[7] KICH_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 91 columns
[8] KICH_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[9] KICH_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 91 columns
[10] KICH_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18122 rows and 91 columns
[11] KICH_Methylation-20160128: SummarizedExperiment with 485577 rows and 66 columns
> rownames( KICH )
CharacterList of length 11
[["KICH_CNASNP-20160128"]] character(0)
[["KICH_CNVSNP-20160128"]] character(0)
[["KICH_GISTIC_AllByGene-20160128"]] character(0)
[["KICH_GISTIC_Peaks-20160128"]] 1 2
[["KICH_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KICH_Mutation-20160128"]] character(0)
[["KICH_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KICH_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["KICH_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KICH_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<1 more element>
> colnames( KICH )
CharacterList of length 11
[["KICH_CNASNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_CNVSNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_AllByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_Peaks-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_GISTIC_ThresholdedByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ...
[["KICH_Mutation-20160128"]] TCGA-KL-8323-01A-21D-2310-10 ...
[["KICH_RNASeq2Gene-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ...
[["KICH_RPPAArray-20160128"]] TCGA-KL-8324-01A-21-A421-20 ...
[["KICH_miRNASeqGene-20160128"]] TCGA-KL-8323-01A-21R-2314-13 ...
[["KICH_RNASeq2GeneNorm-20160128"]] TCGA-KL-8323-01 ... TCGA-KO-8417-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 KICH_CNASNP-20160128 1.6 Mb
2 KICH_CNVSNP-20160128 0.3 Mb
3 KICH_GISTIC_AllByGene-20160128 15.9 Mb
4 KICH_GISTIC_Peaks-20160128 0 Mb
5 KICH_GISTIC_ThresholdedByGene-20160128 15.8 Mb
6 KICH_Mutation-20160128 2.6 Mb
7 KICH_RNASeq2Gene-20160128 16.8 Mb
8 KICH_RPPAArray-20160128 0.1 Mb
9 KICH_miRNASeqGene-20160128 0.9 Mb
10 KICH_RNASeq2GeneNorm-20160128 14.8 Mb
11 KICH_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 9 9 2.34 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
17.00 42.00 50.00 51.52 61.75 86.00
vital_status:
0 1
56 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
325 725 855 1001 1158 2172 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30 1366 2713 2320 3138 4676 10
tumor_tissue_site:
kidney
66
pathologic_stage:
stage i stage ii stage iii stage iv
21 25 14 6
pathology_N_stage:
n0 n1 n2 nx
40 3 2 21
pathology_M_stage:
m0 m1 mx NA's
34 2 9 21
gender:
female male
27 39
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2000 2004 2005 2005 2007 2011
radiation_therapy:
no
66
karnofsky_performance_score:
90 100 NA's
3 10 53
histological_type:
kidney chromophobe
66
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 8.00 24.00 25.09 31.00 75.00 55
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1949 1964 1974 1974 1984 1997 58
race:
asian black or african american white
2 4 58
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
4 32 30
Including an additional 718 columns
A document describing the TCGA cancer code
> experiments( KIRC )
ExperimentList class object of length 14:
[1] KIRC_CNASNP-20160128: RaggedExperiment with 488691 rows and 1059 columns
[2] KIRC_CNVSNP-20160128: RaggedExperiment with 85036 rows and 1059 columns
[3] KIRC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[4] KIRC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 26 rows and 528 columns
[5] KIRC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[6] KIRC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[7] KIRC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[8] KIRC_Mutation-20160128: RaggedExperiment with 26369 rows and 437 columns
[9] KIRC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 606 columns
[10] KIRC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 606 columns
[11] KIRC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 537 columns
[12] KIRC_RPPAArray-20160128: SummarizedExperiment with 217 rows and 478 columns
[13] KIRC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 418 columns
[14] KIRC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 480 columns
> rownames( KIRC )
CharacterList of length 14
[["KIRC_CNASNP-20160128"]] character(0)
[["KIRC_CNVSNP-20160128"]] character(0)
[["KIRC_GISTIC_AllByGene-20160128"]] character(0)
[["KIRC_GISTIC_Peaks-20160128"]] 11 12 1 2 13 14 15 16 ... 7 25 26 8 27 28 29
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KIRC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KIRC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRC_Mutation-20160128"]] character(0)
[["KIRC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( KIRC )
CharacterList of length 14
[["KIRC_CNASNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_CNVSNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_AllByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_Peaks-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_miRNASeqGene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37P-13 ...
[["KIRC_mRNAArray-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ...
[["KIRC_Mutation-20160128"]] TCGA-A3-3308-01A-01D-0966-08 ...
[["KIRC_RNASeq2Gene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
[["KIRC_RNASeq2GeneNorm-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRC_CNASNP-20160128 13.4 Mb
2 KIRC_CNVSNP-20160128 2.6 Mb
3 KIRC_GISTIC_AllByGene-20160128 103.4 Mb
4 KIRC_GISTIC_Peaks-20160128 0.2 Mb
5 KIRC_GISTIC_ThresholdedByGene-20160128 103.2 Mb
6 KIRC_miRNASeqGene-20160128 2.8 Mb
7 KIRC_mRNAArray-20160128 12 Mb
8 KIRC_Mutation-20160128 8.2 Mb
9 KIRC_RNASeq2Gene-20160128 97.4 Mb
10 KIRC_RNASeq2GeneNorm-20160128 97.4 Mb
11 KIRC_RNASeqGene-20160128 86.6 Mb
12 KIRC_RPPAArray-20160128 0.9 Mb
13 KIRC_Methylation_methyl27-20160128 4.9 Mb
14 KIRC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
360 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
177.00 177.00 2.24 1.77 2.61
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 52.00 61.00 60.57 70.00 90.00 1
vital_status:
0 1
360 177
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 333.0 819.0 961.2 1432.0 3615.0 360
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 710.5 1454.5 1536.9 2172.0 4537.0 177
tumor_tissue_site:
kidney
537
pathologic_stage:
stage i stage ii stage iii stage iv NA's
269 57 125 84 2
pathology_N_stage:
n0 n1 nx
240 17 280
pathology_M_stage:
m0 m1 mx NA's
426 79 30 2
gender:
female male
191 346
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2004 2006 2006 2007 2013
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 191 1172 1117 1887 2799 510
radiation_therapy:
no yes NA's
142 2 393
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 85.56 100.00 100.00 483
histological_type:
kidney clear cell renal carcinoma
537
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7.00 14.00 30.00 28.33 40.00 65.00 516
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1946 1966 1978 1979 1996 2001 525
race:
asian black or african american white
8 56 466
NA's
7
ethnicity:
hispanic or latino not hispanic or latino NA's
26 359 152
Including an additional 2250 columns
A document describing the TCGA cancer code
> experiments( KIRC )
ExperimentList class object of length 14:
[1] KIRC_CNASNP-20160128: RaggedExperiment with 488691 rows and 1059 columns
[2] KIRC_CNVSNP-20160128: RaggedExperiment with 85036 rows and 1059 columns
[3] KIRC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[4] KIRC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 26 rows and 528 columns
[5] KIRC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns
[6] KIRC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[7] KIRC_Mutation-20160128: RaggedExperiment with 26369 rows and 437 columns
[8] KIRC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 606 columns
[9] KIRC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 537 columns
[10] KIRC_RPPAArray-20160128: SummarizedExperiment with 217 rows and 478 columns
[11] KIRC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[12] KIRC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18292 rows and 606 columns
[13] KIRC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 418 columns
[14] KIRC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 480 columns
> rownames( KIRC )
CharacterList of length 14
[["KIRC_CNASNP-20160128"]] character(0)
[["KIRC_CNVSNP-20160128"]] character(0)
[["KIRC_GISTIC_AllByGene-20160128"]] character(0)
[["KIRC_GISTIC_Peaks-20160128"]] 11 12 1 2 13 14 15 16 ... 7 25 26 8 27 28 29
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KIRC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRC_Mutation-20160128"]] character(0)
[["KIRC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<4 more elements>
> colnames( KIRC )
CharacterList of length 14
[["KIRC_CNASNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_CNVSNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_AllByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_Peaks-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ...
[["KIRC_mRNAArray-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ...
[["KIRC_Mutation-20160128"]] TCGA-A3-3308-01A-01D-0966-08 ...
[["KIRC_RNASeq2Gene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
[["KIRC_RNASeqGene-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ...
[["KIRC_RPPAArray-20160128"]] TCGA-3Z-A93Z-01A-21-A45H-20 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRC_CNASNP-20160128 13.4 Mb
2 KIRC_CNVSNP-20160128 2.6 Mb
3 KIRC_GISTIC_AllByGene-20160128 103.4 Mb
4 KIRC_GISTIC_Peaks-20160128 0.2 Mb
5 KIRC_GISTIC_ThresholdedByGene-20160128 103.2 Mb
6 KIRC_mRNAArray-20160128 12 Mb
7 KIRC_Mutation-20160128 8.2 Mb
8 KIRC_RNASeq2Gene-20160128 97.4 Mb
9 KIRC_RNASeqGene-20160128 86.6 Mb
10 KIRC_RPPAArray-20160128 0.9 Mb
11 KIRC_miRNASeqGene-20160128 2.8 Mb
12 KIRC_RNASeq2GeneNorm-20160128 86.9 Mb
13 KIRC_Methylation_methyl27-20160128 4.9 Mb
14 KIRC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
360 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 177 177 2.24 1.77 2.61
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 52.00 61.00 60.57 70.00 90.00 1
vital_status:
0 1
360 177
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.0 333.0 819.0 961.2 1432.0 3615.0 360
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 710.5 1454.5 1536.9 2172.0 4537.0 177
tumor_tissue_site:
kidney
537
pathologic_stage:
stage i stage ii stage iii stage iv NA's
269 57 125 84 2
pathology_N_stage:
n0 n1 nx
240 17 280
pathology_M_stage:
m0 m1 mx NA's
426 79 30 2
gender:
female male
191 346
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2004 2006 2006 2007 2013
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 191 1172 1117 1887 2799 510
radiation_therapy:
no yes NA's
142 2 393
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 85.56 100.00 100.00 483
histological_type:
kidney clear cell renal carcinoma
537
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7.00 14.00 30.00 28.33 40.00 65.00 516
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1946 1966 1978 1979 1996 2001 525
race:
asian black or african american white
8 56 466
NA's
7
ethnicity:
hispanic or latino not hispanic or latino NA's
26 359 152
Including an additional 2250 columns
A document describing the TCGA cancer code
> experiments( KIRP )
ExperimentList class object of length 14:
[1] KIRP_CNASNP-20160128: RaggedExperiment with 300681 rows and 593 columns
[2] KIRP_CNVSNP-20160128: RaggedExperiment with 46914 rows and 590 columns
[3] KIRP_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[4] KIRP_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 28 rows and 288 columns
[5] KIRP_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[6] KIRP_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[7] KIRP_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 16 columns
[8] KIRP_Mutation-20160128: RaggedExperiment with 15585 rows and 161 columns
[9] KIRP_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 323 columns
[10] KIRP_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 323 columns
[11] KIRP_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 14 columns
[12] KIRP_RPPAArray-20160128: SummarizedExperiment with 195 rows and 216 columns
[13] KIRP_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 21 columns
[14] KIRP_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 321 columns
> rownames( KIRP )
CharacterList of length 14
[["KIRP_CNASNP-20160128"]] character(0)
[["KIRP_CNVSNP-20160128"]] character(0)
[["KIRP_GISTIC_AllByGene-20160128"]] character(0)
[["KIRP_GISTIC_Peaks-20160128"]] 8 9 1 10 2 11 12 3 ... 22 24 25 7 26 27 28
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KIRP_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KIRP_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRP_Mutation-20160128"]] character(0)
[["KIRP_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRP_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( KIRP )
CharacterList of length 14
[["KIRP_CNASNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_CNVSNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_AllByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_Peaks-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_miRNASeqGene-20160128"]] TCGA-2K-A9WE-01A-11R-A38N-13 ...
[["KIRP_mRNAArray-20160128"]] TCGA-AL-3466-01A-01R-1193-07 ...
[["KIRP_Mutation-20160128"]] TCGA-A4-7286-01A-11D-2136-08 ...
[["KIRP_RNASeq2Gene-20160128"]] TCGA-2K-A9WE-01A-11R-A38C-07 ...
[["KIRP_RNASeq2GeneNorm-20160128"]] TCGA-2K-A9WE-01A-11R-A38C-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRP_CNASNP-20160128 8.2 Mb
2 KIRP_CNVSNP-20160128 1.4 Mb
3 KIRP_GISTIC_AllByGene-20160128 58 Mb
4 KIRP_GISTIC_Peaks-20160128 0.2 Mb
5 KIRP_GISTIC_ThresholdedByGene-20160128 57.8 Mb
6 KIRP_miRNASeqGene-20160128 2.8 Mb
7 KIRP_mRNAArray-20160128 4.4 Mb
8 KIRP_Mutation-20160128 10.6 Mb
9 KIRP_RNASeq2Gene-20160128 53.1 Mb
10 KIRP_RNASeq2GeneNorm-20160128 53.1 Mb
11 KIRP_RNASeqGene-20160128 4.7 Mb
12 KIRP_RPPAArray-20160128 0.4 Mb
13 KIRP_Methylation_methyl27-20160128 4.9 Mb
14 KIRP_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
44.00 44.00 1.76 1.35 3.60
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 53.25 61.50 61.52 71.00 88.00 5
vital_status:
0 1
247 44
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
122.0 341.2 641.0 989.8 1498.5 2941.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 438.2 774.5 1070.2 1513.0 5925.0 45
tumor_tissue_site:
kidney
291
pathologic_stage:
stage i stage ii stage iii stage iv NA's
173 21 52 15 30
pathology_N_stage:
n0 n1 n2 nx NA's
50 24 4 212 1
pathology_M_stage:
m0 m1 mx NA's
95 9 172 15
gender:
female male
77 214
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2008 2011 2010 2012 2013 25
days_to_last_known_alive:
34 NA's
1 290
radiation_therapy:
no yes NA's
209 1 81
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 87.66 100.00 100.00 214
histological_type:
kidney papillary renal cell carcinoma
291
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.00 15.00 24.50 31.73 41.25 185.00 215
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1941 1961 1970 1972 1984 2010 235
race:
american indian or alaska native asian
2 6
black or african american white
61 207
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
12 243 36
Including an additional 1686 columns
A document describing the TCGA cancer code
> experiments( KIRP )
ExperimentList class object of length 14:
[1] KIRP_CNASNP-20160128: RaggedExperiment with 300681 rows and 593 columns
[2] KIRP_CNVSNP-20160128: RaggedExperiment with 46914 rows and 590 columns
[3] KIRP_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[4] KIRP_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 28 rows and 288 columns
[5] KIRP_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns
[6] KIRP_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 16 columns
[7] KIRP_Mutation-20160128: RaggedExperiment with 15585 rows and 161 columns
[8] KIRP_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 323 columns
[9] KIRP_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 14 columns
[10] KIRP_RPPAArray-20160128: SummarizedExperiment with 195 rows and 216 columns
[11] KIRP_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns
[12] KIRP_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18059 rows and 323 columns
[13] KIRP_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 21 columns
[14] KIRP_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 321 columns
> rownames( KIRP )
CharacterList of length 14
[["KIRP_CNASNP-20160128"]] character(0)
[["KIRP_CNVSNP-20160128"]] character(0)
[["KIRP_GISTIC_AllByGene-20160128"]] character(0)
[["KIRP_GISTIC_Peaks-20160128"]] 8 9 1 10 2 11 12 3 ... 22 24 25 7 26 27 28
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["KIRP_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["KIRP_Mutation-20160128"]] character(0)
[["KIRP_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRP_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRP_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<4 more elements>
> colnames( KIRP )
CharacterList of length 14
[["KIRP_CNASNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_CNVSNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_AllByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_Peaks-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_GISTIC_ThresholdedByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ...
[["KIRP_mRNAArray-20160128"]] TCGA-AL-3466-01A-01R-1193-07 ...
[["KIRP_Mutation-20160128"]] TCGA-A4-7286-01A-11D-2136-08 ...
[["KIRP_RNASeq2Gene-20160128"]] TCGA-2K-A9WE-01A-11R-A38C-07 ...
[["KIRP_RNASeqGene-20160128"]] TCGA-AL-3466-01A-02R-1351-07 ...
[["KIRP_RPPAArray-20160128"]] TCGA-2K-A9WE-01A-21-A39N-20 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 KIRP_CNASNP-20160128 8.2 Mb
2 KIRP_CNVSNP-20160128 1.4 Mb
3 KIRP_GISTIC_AllByGene-20160128 58 Mb
4 KIRP_GISTIC_Peaks-20160128 0.2 Mb
5 KIRP_GISTIC_ThresholdedByGene-20160128 57.8 Mb
6 KIRP_mRNAArray-20160128 4.4 Mb
7 KIRP_Mutation-20160128 10.6 Mb
8 KIRP_RNASeq2Gene-20160128 53.1 Mb
9 KIRP_RNASeqGene-20160128 4.7 Mb
10 KIRP_RPPAArray-20160128 0.4 Mb
11 KIRP_miRNASeqGene-20160128 2.8 Mb
12 KIRP_RNASeq2GeneNorm-20160128 46.8 Mb
13 KIRP_Methylation_methyl27-20160128 4.9 Mb
14 KIRP_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 44 44 1.76 1.35 3.6
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
28.00 53.25 61.50 61.52 71.00 88.00 5
vital_status:
0 1
247 44
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
122.0 341.2 641.0 989.8 1498.5 2941.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 438.2 774.5 1070.2 1513.0 5925.0 45
tumor_tissue_site:
kidney
291
pathologic_stage:
stage i stage ii stage iii stage iv NA's
173 21 52 15 30
pathology_N_stage:
n0 n1 n2 nx NA's
50 24 4 212 1
pathology_M_stage:
m0 m1 mx NA's
95 9 172 15
gender:
female male
77 214
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2008 2011 2010 2012 2013 25
days_to_last_known_alive:
34 NA's
1 290
radiation_therapy:
no yes NA's
209 1 81
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 90.00 90.00 87.66 100.00 100.00 214
histological_type:
kidney papillary renal cell carcinoma
291
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.00 15.00 24.50 31.73 41.25 185.00 215
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1941 1961 1970 1972 1984 2010 235
race:
american indian or alaska native asian
2 6
black or african american white
61 207
NA's
15
ethnicity:
hispanic or latino not hispanic or latino NA's
12 243 36
Including an additional 1686 columns
A document describing the TCGA cancer code
> experiments( LAML )
ExperimentList class object of length 11:
[1] LAML_CNASNP-20160128: RaggedExperiment with 874897 rows and 392 columns
[2] LAML_CNVSNP-20160128: RaggedExperiment with 28324 rows and 380 columns
[3] LAML_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[4] LAML_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 191 columns
[5] LAML_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[6] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns
[7] LAML_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 173 columns
[8] LAML_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 173 columns
[9] LAML_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 179 columns
[10] LAML_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 194 columns
[11] LAML_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 194 columns
> rownames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] character(0)
[["LAML_CNVSNP-20160128"]] character(0)
[["LAML_GISTIC_AllByGene-20160128"]] character(0)
[["LAML_GISTIC_Peaks-20160128"]] 1 5 6 7 8 9 2 10 11 12 13 14 15 3 16 4
[["LAML_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LAML_Mutation-20160128"]] character(0)
[["LAML_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeqGene-20160128"]] AADACL3 AADACL4 ABCA4 ... XGPY2 XKRY2 ZFY
[["LAML_Methylation_methyl27-20160128"]] cg00000292 cg00002426 ... cg27665659
...
<1 more element>
> colnames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] TCGA-AB-2802-03A-01D-0756-21 ...
[["LAML_CNVSNP-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_AllByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_Peaks-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_ThresholdedByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_Mutation-20160128"]] TCGA-AB-2802-03B-01W-0728-08 ...
[["LAML_RNASeq2Gene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeq2GeneNorm-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeqGene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_Methylation_methyl27-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 LAML_CNASNP-20160128 23.5 Mb
2 LAML_CNVSNP-20160128 0.9 Mb
3 LAML_GISTIC_AllByGene-20160128 39.5 Mb
4 LAML_GISTIC_Peaks-20160128 0.1 Mb
5 LAML_GISTIC_ThresholdedByGene-20160128 39.5 Mb
6 LAML_Mutation-20160128 2.8 Mb
7 LAML_RNASeq2Gene-20160128 29.6 Mb
8 LAML_RNASeq2GeneNorm-20160128 29.6 Mb
9 LAML_RNASeqGene-20160128 29.8 Mb
10 LAML_Methylation_methyl27-20160128 4.9 Mb
11 LAML_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
80 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
120.000 120.000 0.748 0.586 0.918
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
18.00 44.75 57.00 55.02 67.00 88.00
vital_status:
0 1
67 133
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 91.5 273.0 355.7 489.0 1706.0 80
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 296.2 699.0 913.5 1506.8 2861.0 132
tumor_tissue_site:
bone marrow NA's
199 1
gender:
female male
91 109
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2001 2004 2006 2006 2008 2010
race:
asian black or african american white
2 15 181
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
3 194 3
Including an additional 478 columns
A document describing the TCGA cancer code
> experiments( LAML )
ExperimentList class object of length 11:
[1] LAML_CNASNP-20160128: RaggedExperiment with 874897 rows and 392 columns
[2] LAML_CNVSNP-20160128: RaggedExperiment with 28324 rows and 380 columns
[3] LAML_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[4] LAML_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 191 columns
[5] LAML_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns
[6] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns
[7] LAML_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 173 columns
[8] LAML_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 179 columns
[9] LAML_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17258 rows and 173 columns
[10] LAML_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 194 columns
[11] LAML_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 194 columns
> rownames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] character(0)
[["LAML_CNVSNP-20160128"]] character(0)
[["LAML_GISTIC_AllByGene-20160128"]] character(0)
[["LAML_GISTIC_Peaks-20160128"]] 1 5 6 7 8 9 2 10 11 12 13 14 15 3 16 4
[["LAML_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LAML_Mutation-20160128"]] character(0)
[["LAML_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_RNASeqGene-20160128"]] AADACL3 AADACL4 ABCA4 ... XGPY2 XKRY2 ZFY
[["LAML_RNASeq2GeneNorm-20160128"]] A1BG A2LD1 A2ML1 ... ZZZ3 psiTPTE22 tAKR
[["LAML_Methylation_methyl27-20160128"]] cg00000292 cg00002426 ... cg27665659
...
<1 more element>
> colnames( LAML )
CharacterList of length 11
[["LAML_CNASNP-20160128"]] TCGA-AB-2802-03A-01D-0756-21 ...
[["LAML_CNVSNP-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_AllByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_Peaks-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_GISTIC_ThresholdedByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ...
[["LAML_Mutation-20160128"]] TCGA-AB-2802-03B-01W-0728-08 ...
[["LAML_RNASeq2Gene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeqGene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ...
[["LAML_RNASeq2GeneNorm-20160128"]] TCGA-AB-2803-03 ... TCGA-AB-3012-03
[["LAML_Methylation_methyl27-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 LAML_CNASNP-20160128 23.5 Mb
2 LAML_CNVSNP-20160128 0.9 Mb
3 LAML_GISTIC_AllByGene-20160128 39.5 Mb
4 LAML_GISTIC_Peaks-20160128 0.1 Mb
5 LAML_GISTIC_ThresholdedByGene-20160128 39.5 Mb
6 LAML_Mutation-20160128 2.8 Mb
7 LAML_RNASeq2Gene-20160128 29.6 Mb
8 LAML_RNASeqGene-20160128 29.8 Mb
9 LAML_RNASeq2GeneNorm-20160128 24.9 Mb
10 LAML_Methylation_methyl27-20160128 4.9 Mb
11 LAML_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
80 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 120 120 0.748 0.586 0.918
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
18.00 44.75 57.00 55.02 67.00 88.00
vital_status:
0 1
67 133
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 91.5 273.0 355.7 489.0 1706.0 80
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 296.2 699.0 913.5 1506.8 2861.0 132
tumor_tissue_site:
bone marrow NA's
199 1
gender:
female male
91 109
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2001 2004 2006 2006 2008 2010
race:
asian black or african american white
2 15 181
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
3 194 3
Including an additional 478 columns
A document describing the TCGA cancer code
> experiments( LGG )
ExperimentList class object of length 13:
[1] LGG_CNASeq-20160128: RaggedExperiment with 6360 rows and 104 columns
[2] LGG_CNASNP-20160128: RaggedExperiment with 411918 rows and 1015 columns
[3] LGG_CNVSNP-20160128: RaggedExperiment with 79791 rows and 1015 columns
[4] LGG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[5] LGG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 46 rows and 513 columns
[6] LGG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[7] LGG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 526 columns
[8] LGG_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 27 columns
[9] LGG_Mutation-20160128: RaggedExperiment with 9885 rows and 286 columns
[10] LGG_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 530 columns
[11] LGG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 530 columns
[12] LGG_RPPAArray-20160128: SummarizedExperiment with 201 rows and 435 columns
[13] LGG_Methylation-20160128: SummarizedExperiment with 485577 rows and 530 columns
> rownames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] character(0)
[["LGG_CNASNP-20160128"]] character(0)
[["LGG_CNVSNP-20160128"]] character(0)
[["LGG_GISTIC_AllByGene-20160128"]] character(0)
[["LGG_GISTIC_Peaks-20160128"]] 21 22 1 2 23 3 24 25 ... 45 16 17 46 18 47 48
[["LGG_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LGG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LGG_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LGG_Mutation-20160128"]] character(0)
[["LGG_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] TCGA-CS-4938-01B-11D-1891-02 ...
[["LGG_CNASNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_CNVSNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_AllByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_Peaks-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_ThresholdedByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_miRNASeqGene-20160128"]] TCGA-CS-4938-01B-11R-1895-13 ...
[["LGG_mRNAArray-20160128"]] TCGA-CS-4942-01A-01R-1470-07 ...
[["LGG_Mutation-20160128"]] TCGA-CS-4938-01B-11D-1893-08 ...
[["LGG_RNASeq2Gene-20160128"]] TCGA-CS-4938-01B-11R-1896-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LGG_CNASeq-20160128 0.2 Mb
2 LGG_CNASNP-20160128 11.3 Mb
3 LGG_CNVSNP-20160128 2.4 Mb
4 LGG_GISTIC_AllByGene-20160128 100.5 Mb
5 LGG_GISTIC_Peaks-20160128 0.3 Mb
6 LGG_GISTIC_ThresholdedByGene-20160128 100.4 Mb
7 LGG_miRNASeqGene-20160128 4.4 Mb
8 LGG_mRNAArray-20160128 5.9 Mb
9 LGG_Mutation-20160128 4.2 Mb
10 LGG_RNASeq2Gene-20160128 85.5 Mb
11 LGG_RNASeq2GeneNorm-20160128 85.5 Mb
12 LGG_RPPAArray-20160128 0.8 Mb
13 LGG_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
391 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
125.00 125.00 2.23 1.87 2.83
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.00 32.00 41.00 42.93 53.00 86.00 2
vital_status:
0 1 NA's
389 126 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7 438 814 1219 1547 5166 391
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-1.0 384.0 629.0 880.1 1147.0 6423.0 127
tumor_tissue_site:
central nervous system NA's
515 1
gender:
female male NA's
230 285 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2008 2011 2009 2012 2013 1
radiation_therapy:
no yes NA's
186 296 34
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 80.00 90.00 86.64 100.00 100.00 209
histological_type:
astrocytoma oligoastrocytoma oligodendroglioma NA's
194 130 191 1
race:
american indian or alaska native asian
1 8
black or african american white
21 475
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
32 449 35
Including an additional 1764 columns
A document describing the TCGA cancer code
> experiments( LGG )
ExperimentList class object of length 13:
[1] LGG_CNASeq-20160128: RaggedExperiment with 6360 rows and 104 columns
[2] LGG_CNASNP-20160128: RaggedExperiment with 411918 rows and 1015 columns
[3] LGG_CNVSNP-20160128: RaggedExperiment with 79791 rows and 1015 columns
[4] LGG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[5] LGG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 46 rows and 513 columns
[6] LGG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 513 columns
[7] LGG_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 27 columns
[8] LGG_Mutation-20160128: RaggedExperiment with 9885 rows and 286 columns
[9] LGG_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 530 columns
[10] LGG_RPPAArray-20160128: SummarizedExperiment with 201 rows and 435 columns
[11] LGG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 526 columns
[12] LGG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18311 rows and 530 columns
[13] LGG_Methylation-20160128: SummarizedExperiment with 485577 rows and 530 columns
> rownames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] character(0)
[["LGG_CNASNP-20160128"]] character(0)
[["LGG_CNVSNP-20160128"]] character(0)
[["LGG_GISTIC_AllByGene-20160128"]] character(0)
[["LGG_GISTIC_Peaks-20160128"]] 21 22 1 2 23 3 24 25 ... 45 16 17 46 18 47 48
[["LGG_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LGG_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LGG_Mutation-20160128"]] character(0)
[["LGG_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LGG_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( LGG )
CharacterList of length 13
[["LGG_CNASeq-20160128"]] TCGA-CS-4938-01B-11D-1891-02 ...
[["LGG_CNASNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_CNVSNP-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_AllByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_Peaks-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_GISTIC_ThresholdedByGene-20160128"]] TCGA-CS-4938-01B-11D-1892-01 ...
[["LGG_mRNAArray-20160128"]] TCGA-CS-4942-01A-01R-1470-07 ...
[["LGG_Mutation-20160128"]] TCGA-CS-4938-01B-11D-1893-08 ...
[["LGG_RNASeq2Gene-20160128"]] TCGA-CS-4938-01B-11R-1896-07 ...
[["LGG_RPPAArray-20160128"]] TCGA-CS-4938-01B-11-A300-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LGG_CNASeq-20160128 0.2 Mb
2 LGG_CNASNP-20160128 11.3 Mb
3 LGG_CNVSNP-20160128 2.4 Mb
4 LGG_GISTIC_AllByGene-20160128 100.5 Mb
5 LGG_GISTIC_Peaks-20160128 0.3 Mb
6 LGG_GISTIC_ThresholdedByGene-20160128 100.4 Mb
7 LGG_mRNAArray-20160128 5.9 Mb
8 LGG_Mutation-20160128 4.2 Mb
9 LGG_RNASeq2Gene-20160128 85.5 Mb
10 LGG_RPPAArray-20160128 0.8 Mb
11 LGG_miRNASeqGene-20160128 4.4 Mb
12 LGG_RNASeq2GeneNorm-20160128 76.4 Mb
13 LGG_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
391 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 125 125 2.23 1.87 2.83
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.00 32.00 41.00 42.93 53.00 86.00 2
vital_status:
0 1 NA's
389 126 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
7 438 814 1219 1547 5166 391
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-1.0 384.0 629.0 880.1 1147.0 6423.0 127
tumor_tissue_site:
central nervous system NA's
515 1
gender:
female male NA's
230 285 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2008 2011 2009 2012 2013 1
radiation_therapy:
no yes NA's
186 296 34
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 80.00 90.00 86.64 100.00 100.00 209
histological_type:
astrocytoma oligoastrocytoma oligodendroglioma NA's
194 130 191 1
race:
american indian or alaska native asian
1 8
black or african american white
21 475
NA's
11
ethnicity:
hispanic or latino not hispanic or latino NA's
32 449 35
Including an additional 1764 columns
A document describing the TCGA cancer code
> experiments( LIHC )
ExperimentList class object of length 12:
[1] LIHC_CNASNP-20160128: RaggedExperiment with 363628 rows and 760 columns
[2] LIHC_CNVSNP-20160128: RaggedExperiment with 93328 rows and 760 columns
[3] LIHC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[4] LIHC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 59 rows and 370 columns
[5] LIHC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[6] LIHC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns
[7] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
[8] LIHC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 423 columns
[9] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 423 columns
[10] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns
[11] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns
[12] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns
> rownames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] character(0)
[["LIHC_CNVSNP-20160128"]] character(0)
[["LIHC_GISTIC_AllByGene-20160128"]] character(0)
[["LIHC_GISTIC_Peaks-20160128"]] 28 29 1 2 3 30 4 31 ... 23 24 58 25 26 59 60
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LIHC_Mutation-20160128"]] character(0)
[["LIHC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_CNVSNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_AllByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_Peaks-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ...
[["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ...
[["LIHC_RNASeq2Gene-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ...
[["LIHC_RNASeq2GeneNorm-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ...
[["LIHC_RNASeqGene-20160128"]] TCGA-BC-4073-01B-02R-A131-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LIHC_CNASNP-20160128 9.9 Mb
2 LIHC_CNVSNP-20160128 2.7 Mb
3 LIHC_GISTIC_AllByGene-20160128 73.5 Mb
4 LIHC_GISTIC_Peaks-20160128 0.3 Mb
5 LIHC_GISTIC_ThresholdedByGene-20160128 73.3 Mb
6 LIHC_miRNASeqGene-20160128 3.6 Mb
7 LIHC_Mutation-20160128 16.8 Mb
8 LIHC_RNASeq2Gene-20160128 68.8 Mb
9 LIHC_RNASeq2GeneNorm-20160128 68.8 Mb
10 LIHC_RNASeqGene-20160128 6.6 Mb
11 LIHC_RPPAArray-20160128 0.4 Mb
12 LIHC_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
245 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
132.000 132.000 1.144 0.956 1.633
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16.00 51.00 61.00 59.27 69.00 87.00 4
vital_status:
0 1
245 132
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 194.8 417.5 672.1 837.0 3258.0 245
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 395.8 649.5 885.8 1222.0 3675.0 133
tumor_tissue_site:
liver
377
pathology_N_stage:
n0 n1 nx NA's
257 4 115 1
pathology_M_stage:
m0 m1 mx
272 4 101
gender:
female male
122 255
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2008 2011 2010 2012 2013 3
radiation_therapy:
no yes NA's
345 9 23
histological_type:
fibrolamellar carcinoma hepatocellular carcinoma
3 367
hepatocholangiocarcinoma (mixed)
7
residual_tumor:
r0 r1 r2 rx NA's
330 17 1 22 7
race:
american indian or alaska native asian
2 161
black or african american white
17 187
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
18 340 19
Including an additional 1218 columns
A document describing the TCGA cancer code
> experiments( LIHC )
ExperimentList class object of length 12:
[1] LIHC_CNASNP-20160128: RaggedExperiment with 363628 rows and 760 columns
[2] LIHC_CNVSNP-20160128: RaggedExperiment with 93328 rows and 760 columns
[3] LIHC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[4] LIHC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 59 rows and 370 columns
[5] LIHC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns
[6] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns
[7] LIHC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 423 columns
[8] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns
[9] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns
[10] LIHC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns
[11] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17690 rows and 423 columns
[12] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns
> rownames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] character(0)
[["LIHC_CNVSNP-20160128"]] character(0)
[["LIHC_GISTIC_AllByGene-20160128"]] character(0)
[["LIHC_GISTIC_Peaks-20160128"]] 28 29 1 2 3 30 4 31 ... 23 24 58 25 26 59 60
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LIHC_Mutation-20160128"]] character(0)
[["LIHC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LIHC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( LIHC )
CharacterList of length 12
[["LIHC_CNASNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_CNVSNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_AllByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_Peaks-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ...
[["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ...
[["LIHC_RNASeq2Gene-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ...
[["LIHC_RNASeqGene-20160128"]] TCGA-BC-4073-01B-02R-A131-07 ...
[["LIHC_RPPAArray-20160128"]] TCGA-BC-4072-01B-21-A40L-20 ...
[["LIHC_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LIHC_CNASNP-20160128 9.9 Mb
2 LIHC_CNVSNP-20160128 2.7 Mb
3 LIHC_GISTIC_AllByGene-20160128 73.5 Mb
4 LIHC_GISTIC_Peaks-20160128 0.3 Mb
5 LIHC_GISTIC_ThresholdedByGene-20160128 73.3 Mb
6 LIHC_Mutation-20160128 16.8 Mb
7 LIHC_RNASeq2Gene-20160128 68.8 Mb
8 LIHC_RNASeqGene-20160128 6.6 Mb
9 LIHC_RPPAArray-20160128 0.4 Mb
10 LIHC_miRNASeqGene-20160128 3.6 Mb
11 LIHC_RNASeq2GeneNorm-20160128 59.3 Mb
12 LIHC_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
245 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 132 132 1.14 0.956 1.63
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16.00 51.00 61.00 59.27 69.00 87.00 4
vital_status:
0 1
245 132
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 194.8 417.5 672.1 837.0 3258.0 245
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 395.8 649.5 885.8 1222.0 3675.0 133
tumor_tissue_site:
liver
377
pathology_N_stage:
n0 n1 nx NA's
257 4 115 1
pathology_M_stage:
m0 m1 mx
272 4 101
gender:
female male
122 255
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2008 2011 2010 2012 2013 3
radiation_therapy:
no yes NA's
345 9 23
histological_type:
fibrolamellar carcinoma hepatocellular carcinoma
3 367
hepatocholangiocarcinoma (mixed)
7
residual_tumor:
r0 r1 r2 rx NA's
330 17 1 22 7
race:
american indian or alaska native asian
2 161
black or african american white
17 187
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
18 340 19
Including an additional 1218 columns
A document describing the TCGA cancer code
> experiments( LUAD )
ExperimentList class object of length 15:
[1] LUAD_CNASeq-20160128: RaggedExperiment with 399592 rows and 249 columns
[2] LUAD_CNASNP-20160128: RaggedExperiment with 501475 rows and 1095 columns
[3] LUAD_CNVSNP-20160128: RaggedExperiment with 115836 rows and 1095 columns
[4] LUAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[5] LUAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 73 rows and 516 columns
[6] LUAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[7] LUAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 498 columns
[8] LUAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 32 columns
[9] LUAD_Mutation-20160128: RaggedExperiment with 72541 rows and 230 columns
[10] LUAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 576 columns
[11] LUAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 576 columns
[12] LUAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 162 columns
[13] LUAD_RPPAArray-20160128: SummarizedExperiment with 223 rows and 365 columns
[14] LUAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 89 columns
[15] LUAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 492 columns
> rownames( LUAD )
CharacterList of length 15
[["LUAD_CNASeq-20160128"]] character(0)
[["LUAD_CNASNP-20160128"]] character(0)
[["LUAD_CNVSNP-20160128"]] character(0)
[["LUAD_GISTIC_AllByGene-20160128"]] character(0)
[["LUAD_GISTIC_Peaks-20160128"]] 30 1 31 2 32 33 34 ... 71 26 72 27 73 28 74
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LUAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LUAD_Mutation-20160128"]] character(0)
[["LUAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<5 more elements>
> colnames( LUAD )
CharacterList of length 15
[["LUAD_CNASeq-20160128"]] TCGA-05-4249-01A-01D-1103-02 ...
[["LUAD_CNASNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_CNVSNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_AllByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_Peaks-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_miRNASeqGene-20160128"]] TCGA-05-4384-01A-01T-1754-13 ...
[["LUAD_mRNAArray-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
[["LUAD_Mutation-20160128"]] TCGA-05-4249-01A-01D-1105-08 ...
[["LUAD_RNASeq2Gene-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
...
<5 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUAD_CNASeq-20160128 10.8 Mb
2 LUAD_CNASNP-20160128 13.7 Mb
3 LUAD_CNVSNP-20160128 3.4 Mb
4 LUAD_GISTIC_AllByGene-20160128 101.2 Mb
5 LUAD_GISTIC_Peaks-20160128 0.5 Mb
6 LUAD_GISTIC_ThresholdedByGene-20160128 101 Mb
7 LUAD_miRNASeqGene-20160128 4.2 Mb
8 LUAD_mRNAArray-20160128 6.6 Mb
9 LUAD_Mutation-20160128 92.9 Mb
10 LUAD_RNASeq2Gene-20160128 92.7 Mb
11 LUAD_RNASeq2GeneNorm-20160128 92.7 Mb
12 LUAD_RNASeqGene-20160128 27.9 Mb
13 LUAD_RPPAArray-20160128 0.7 Mb
14 LUAD_Methylation_methyl27-20160128 4.9 Mb
15 LUAD_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
336 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
184.00 184.00 1.70 1.37 2.00
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
33.00 59.00 66.00 65.22 72.00 88.00 31
vital_status:
0 1
332 188
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 297.8 619.0 791.4 1120.0 4961.0 336
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 459.5 670.0 968.7 1139.0 7248.0 193
tumor_tissue_site:
lung
520
gender:
female male
279 241
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1991 2007 2010 2008 2011 2013 19
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 96.5 141.0 327.6 386.0 1178.0 513
radiation_therapy:
no yes NA's
413 61 46
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 78.55 100.00 100.00 382
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.50 40.00 41.79 50.00 154.00 165
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1930 1956 1965 1965 1972 1999 241
residual_tumor:
r0 r1 r2 rx NA's
347 13 4 26 130
race:
american indian or alaska native asian
1 8
black or african american white
53 392
NA's
66
ethnicity:
hispanic or latino not hispanic or latino NA's
7 388 125
Including an additional 2607 columns
A document describing the TCGA cancer code
> experiments( LUAD )
ExperimentList class object of length 15:
[1] LUAD_CNASeq-20160128: RaggedExperiment with 399592 rows and 249 columns
[2] LUAD_CNASNP-20160128: RaggedExperiment with 501475 rows and 1095 columns
[3] LUAD_CNVSNP-20160128: RaggedExperiment with 115836 rows and 1095 columns
[4] LUAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[5] LUAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 73 rows and 516 columns
[6] LUAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 516 columns
[7] LUAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 32 columns
[8] LUAD_Mutation-20160128: RaggedExperiment with 72541 rows and 230 columns
[9] LUAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 576 columns
[10] LUAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 162 columns
[11] LUAD_RPPAArray-20160128: SummarizedExperiment with 223 rows and 365 columns
[12] LUAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 498 columns
[13] LUAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18289 rows and 576 columns
[14] LUAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 89 columns
[15] LUAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 492 columns
> rownames( LUAD )
CharacterList of length 15
[["LUAD_CNASeq-20160128"]] character(0)
[["LUAD_CNASNP-20160128"]] character(0)
[["LUAD_CNVSNP-20160128"]] character(0)
[["LUAD_GISTIC_AllByGene-20160128"]] character(0)
[["LUAD_GISTIC_Peaks-20160128"]] 30 1 31 2 32 33 34 ... 71 26 72 27 73 28 74
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LUAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["LUAD_Mutation-20160128"]] character(0)
[["LUAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["LUAD_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<5 more elements>
> colnames( LUAD )
CharacterList of length 15
[["LUAD_CNASeq-20160128"]] TCGA-05-4249-01A-01D-1103-02 ...
[["LUAD_CNASNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_CNVSNP-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_AllByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_Peaks-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-05-4244-01A-01D-1877-01 ...
[["LUAD_mRNAArray-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
[["LUAD_Mutation-20160128"]] TCGA-05-4249-01A-01D-1105-08 ...
[["LUAD_RNASeq2Gene-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
[["LUAD_RNASeqGene-20160128"]] TCGA-05-4244-01A-01R-1107-07 ...
...
<5 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUAD_CNASeq-20160128 10.8 Mb
2 LUAD_CNASNP-20160128 13.7 Mb
3 LUAD_CNVSNP-20160128 3.4 Mb
4 LUAD_GISTIC_AllByGene-20160128 101.2 Mb
5 LUAD_GISTIC_Peaks-20160128 0.5 Mb
6 LUAD_GISTIC_ThresholdedByGene-20160128 101 Mb
7 LUAD_mRNAArray-20160128 6.6 Mb
8 LUAD_Mutation-20160128 92.9 Mb
9 LUAD_RNASeq2Gene-20160128 92.7 Mb
10 LUAD_RNASeqGene-20160128 27.9 Mb
11 LUAD_RPPAArray-20160128 0.7 Mb
12 LUAD_miRNASeqGene-20160128 4.2 Mb
13 LUAD_RNASeq2GeneNorm-20160128 82.7 Mb
14 LUAD_Methylation_methyl27-20160128 4.9 Mb
15 LUAD_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
336 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 184 184 1.7 1.37 2
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
33.00 59.00 66.00 65.22 72.00 88.00 31
vital_status:
0 1
332 188
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 297.8 619.0 791.4 1120.0 4961.0 336
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 459.5 670.0 968.7 1139.0 7248.0 193
tumor_tissue_site:
lung
520
gender:
female male
279 241
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1991 2007 2010 2008 2011 2013 19
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 96.5 141.0 327.6 386.0 1178.0 513
radiation_therapy:
no yes NA's
413 61 46
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 78.55 100.00 100.00 382
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.50 40.00 41.79 50.00 154.00 165
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1930 1956 1965 1965 1972 1999 241
residual_tumor:
r0 r1 r2 rx NA's
347 13 4 26 130
race:
american indian or alaska native asian
1 8
black or african american white
53 392
NA's
66
ethnicity:
hispanic or latino not hispanic or latino NA's
7 388 125
Including an additional 2607 columns
A document describing the TCGA cancer code
> experiments( LUSC )
ExperimentList class object of length 17:
[1] LUSC_CNACGH-20160128: RaggedExperiment with 87417 rows and 407 columns
[2] LUSC_CNASNP-20160128: RaggedExperiment with 543091 rows and 1035 columns
[3] LUSC_CNVSNP-20160128: RaggedExperiment with 134864 rows and 1032 columns
[4] LUSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[5] LUSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 78 rows and 501 columns
[6] LUSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[7] LUSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 387 columns
[8] LUSC_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 112 columns
[9] LUSC_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 154 columns
[10] LUSC_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 133 columns
[11] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
[12] LUSC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 552 columns
[13] LUSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 552 columns
[14] LUSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 240 columns
[15] LUSC_RPPAArray-20160128: SummarizedExperiment with 223 rows and 328 columns
[16] LUSC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 160 columns
[17] LUSC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 412 columns
> rownames( LUSC )
CharacterList of length 17
[["LUSC_CNACGH-20160128"]] character(0)
[["LUSC_CNASNP-20160128"]] character(0)
[["LUSC_CNVSNP-20160128"]] character(0)
[["LUSC_GISTIC_AllByGene-20160128"]] character(0)
[["LUSC_GISTIC_Peaks-20160128"]] 31 32 1 33 2 34 3 ... 27 28 76 77 78 29 79
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LUSC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["LUSC_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["LUSC_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] AACS FSTL1 ELMO2 ... CTSC AQP7
...
<7 more elements>
> colnames( LUSC )
CharacterList of length 17
[["LUSC_CNACGH-20160128"]] TCGA-18-3406-01A-01D-1519-02 ...
[["LUSC_CNASNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_CNVSNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_AllByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_Peaks-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_miRNASeqGene-20160128"]] TCGA-18-5592-01A-01T-1634-13 ...
[["LUSC_mRNAArray_huex-20160128"]] TCGA-18-3406-01A-01R-1030-03 ...
[["LUSC_mRNAArray_TX_g4502a-20160128"]] TCGA-18-3406-01A-01R-0980-07 ...
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] TCGA-18-3406-01A-01R-1031-01 ...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUSC_CNACGH-20160128 2.5 Mb
2 LUSC_CNASNP-20160128 14.8 Mb
3 LUSC_CNVSNP-20160128 3.9 Mb
4 LUSC_GISTIC_AllByGene-20160128 98.3 Mb
5 LUSC_GISTIC_Peaks-20160128 0.5 Mb
6 LUSC_GISTIC_ThresholdedByGene-20160128 98.1 Mb
7 LUSC_miRNASeqGene-20160128 3.3 Mb
8 LUSC_mRNAArray_huex-20160128 18.3 Mb
9 LUSC_mRNAArray_TX_g4502a-20160128 23.2 Mb
10 LUSC_mRNAArray_TX_ht_hg_u133a-20160128 13.7 Mb
11 LUSC_Mutation-20160128 81 Mb
12 LUSC_RNASeq2Gene-20160128 89 Mb
13 LUSC_RNASeq2GeneNorm-20160128 89 Mb
14 LUSC_RNASeqGene-20160128 40.1 Mb
15 LUSC_RPPAArray-20160128 0.6 Mb
16 LUSC_Methylation_methyl27-20160128 4.9 Mb
17 LUSC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
289 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
215.00 215.00 1.51 1.25 1.88
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
39.00 62.00 68.00 67.26 73.00 90.00 10
vital_status:
0 1
284 220
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.0 280.0 550.0 872.3 1110.5 5287.0 289
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 394 757 1049 1374 4765 221
tumor_tissue_site:
lung
504
pathology_N_stage:
n0 n1 n2 n3 nx
320 133 40 5 6
gender:
female male
131 373
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2005 2009 2008 2011 2013 25
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 298.8 706.0 904.8 1051.8 3724.0 436
radiation_therapy:
no yes NA's
387 53 64
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 0.0 80.0 60.3 90.0 100.0 338
histological_type:
lung basaloid squamous cell carcinoma
15
lung papillary squamous cell caricnoma
6
lung small cell squamous cell carcinoma
1
lung squamous cell carcinoma- not otherwise specified (nos)
482
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 31.12 50.00 52.91 64.50 240.00 77
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1933 1952 1960 1960 1968 1997 183
residual_tumor:
r0 r1 r2 rx NA's
401 12 4 23 64
race:
asian black or african american white
9 31 351
NA's
113
ethnicity:
hispanic or latino not hispanic or latino NA's
8 319 177
Including an additional 2238 columns
A document describing the TCGA cancer code
> experiments( LUSC )
ExperimentList class object of length 17:
[1] LUSC_CNACGH-20160128: RaggedExperiment with 87417 rows and 407 columns
[2] LUSC_CNASNP-20160128: RaggedExperiment with 543091 rows and 1035 columns
[3] LUSC_CNVSNP-20160128: RaggedExperiment with 134864 rows and 1032 columns
[4] LUSC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[5] LUSC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 78 rows and 501 columns
[6] LUSC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 501 columns
[7] LUSC_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 112 columns
[8] LUSC_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 154 columns
[9] LUSC_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 133 columns
[10] LUSC_Mutation-20160128: RaggedExperiment with 65305 rows and 178 columns
[11] LUSC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 552 columns
[12] LUSC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 240 columns
[13] LUSC_RPPAArray-20160128: SummarizedExperiment with 223 rows and 328 columns
[14] LUSC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 387 columns
[15] LUSC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18520 rows and 552 columns
[16] LUSC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 160 columns
[17] LUSC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 412 columns
> rownames( LUSC )
CharacterList of length 17
[["LUSC_CNACGH-20160128"]] character(0)
[["LUSC_CNASNP-20160128"]] character(0)
[["LUSC_CNVSNP-20160128"]] character(0)
[["LUSC_GISTIC_AllByGene-20160128"]] character(0)
[["LUSC_GISTIC_Peaks-20160128"]] 31 32 1 33 2 34 3 ... 27 28 76 77 78 29 79
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["LUSC_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["LUSC_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] AACS FSTL1 ELMO2 ... CTSC AQP7
[["LUSC_Mutation-20160128"]] character(0)
...
<7 more elements>
> colnames( LUSC )
CharacterList of length 17
[["LUSC_CNACGH-20160128"]] TCGA-18-3406-01A-01D-1519-02 ...
[["LUSC_CNASNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_CNVSNP-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_AllByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_Peaks-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_GISTIC_ThresholdedByGene-20160128"]] TCGA-18-3406-01A-01D-0978-01 ...
[["LUSC_mRNAArray_huex-20160128"]] TCGA-18-3406-01A-01R-1030-03 ...
[["LUSC_mRNAArray_TX_g4502a-20160128"]] TCGA-18-3406-01A-01R-0980-07 ...
[["LUSC_mRNAArray_TX_ht_hg_u133a-20160128"]] TCGA-18-3406-01A-01R-1031-01 ...
[["LUSC_Mutation-20160128"]] TCGA-18-3406-01A-01D-0983-08 ...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 LUSC_CNACGH-20160128 2.5 Mb
2 LUSC_CNASNP-20160128 14.8 Mb
3 LUSC_CNVSNP-20160128 3.9 Mb
4 LUSC_GISTIC_AllByGene-20160128 98.3 Mb
5 LUSC_GISTIC_Peaks-20160128 0.5 Mb
6 LUSC_GISTIC_ThresholdedByGene-20160128 98.1 Mb
7 LUSC_mRNAArray_huex-20160128 18.3 Mb
8 LUSC_mRNAArray_TX_g4502a-20160128 23.2 Mb
9 LUSC_mRNAArray_TX_ht_hg_u133a-20160128 13.7 Mb
10 LUSC_Mutation-20160128 81 Mb
11 LUSC_RNASeq2Gene-20160128 89 Mb
12 LUSC_RNASeqGene-20160128 40.1 Mb
13 LUSC_RPPAArray-20160128 0.6 Mb
14 LUSC_miRNASeqGene-20160128 3.3 Mb
15 LUSC_RNASeq2GeneNorm-20160128 80.4 Mb
16 LUSC_Methylation_methyl27-20160128 4.9 Mb
17 LUSC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
289 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 215 215 1.51 1.25 1.88
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
39.00 62.00 68.00 67.26 73.00 90.00 10
vital_status:
0 1
284 220
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.0 280.0 550.0 872.3 1110.5 5287.0 289
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 394 757 1049 1374 4765 221
tumor_tissue_site:
lung
504
pathology_N_stage:
n0 n1 n2 n3 nx
320 133 40 5 6
gender:
female male
131 373
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2005 2009 2008 2011 2013 25
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 298.8 706.0 904.8 1051.8 3724.0 436
radiation_therapy:
no yes NA's
387 53 64
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 0.0 80.0 60.3 90.0 100.0 338
histological_type:
lung basaloid squamous cell carcinoma
15
lung papillary squamous cell caricnoma
6
lung small cell squamous cell carcinoma
1
lung squamous cell carcinoma- not otherwise specified (nos)
482
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 31.12 50.00 52.91 64.50 240.00 77
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1933 1952 1960 1960 1968 1997 183
residual_tumor:
r0 r1 r2 rx NA's
401 12 4 23 64
race:
asian black or african american white
9 31 351
NA's
113
ethnicity:
hispanic or latino not hispanic or latino NA's
8 319 177
Including an additional 2238 columns
A document describing the TCGA cancer code
> experiments( MESO )
ExperimentList class object of length 10:
[1] MESO_CNASNP-20160128: RaggedExperiment with 90003 rows and 173 columns
[2] MESO_CNVSNP-20160128: RaggedExperiment with 18335 rows and 172 columns
[3] MESO_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[4] MESO_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 87 columns
[5] MESO_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[6] MESO_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 87 columns
[7] MESO_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 87 columns
[8] MESO_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 87 columns
[9] MESO_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[10] MESO_Methylation-20160128: SummarizedExperiment with 485577 rows and 87 columns
> rownames( MESO )
CharacterList of length 10
[["MESO_CNASNP-20160128"]] character(0)
[["MESO_CNVSNP-20160128"]] character(0)
[["MESO_GISTIC_AllByGene-20160128"]] character(0)
[["MESO_GISTIC_Peaks-20160128"]] 1 2 3 4 5 6 7 8 ... 14 15 16 17 18 19 20 21
[["MESO_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["MESO_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["MESO_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["MESO_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( MESO )
CharacterList of length 10
[["MESO_CNASNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_CNVSNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_AllByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_Peaks-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_ThresholdedByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_miRNASeqGene-20160128"]] TCGA-3H-AB3K-01A-11R-A404-13 ...
[["MESO_RNASeq2Gene-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RNASeq2GeneNorm-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RPPAArray-20160128"]] TCGA-3H-AB3K-01A-21-A45O-20 ...
[["MESO_Methylation-20160128"]] TCGA-3H-AB3K-01A-11D-A39S-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 MESO_CNASNP-20160128 2.5 Mb
2 MESO_CNVSNP-20160128 0.6 Mb
3 MESO_GISTIC_AllByGene-20160128 19.9 Mb
4 MESO_GISTIC_Peaks-20160128 0.1 Mb
5 MESO_GISTIC_ThresholdedByGene-20160128 19.8 Mb
6 MESO_miRNASeqGene-20160128 0.9 Mb
7 MESO_RNASeq2Gene-20160128 16.2 Mb
8 MESO_RNASeq2GeneNorm-20160128 16.2 Mb
9 MESO_RPPAArray-20160128 0.1 Mb
10 MESO_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
14 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
73.00 73.00 1.25 1.11 1.67
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 57.00 64.00 62.99 69.00 81.00
vital_status:
0 1
13 74
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 253.0 457.0 584.1 789.0 2790.0 14
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-8 499 1168 1091 1490 2359 74
tumor_tissue_site:
pleura
87
pathology_N_stage:
n0 n1 n2 n3 nx
44 10 26 3 4
pathology_M_stage:
m0 m1 mx
57 3 27
gender:
female male
16 71
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2008 2010 2009 2012 2013
radiation_therapy:
no yes NA's
62 24 1
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 77.65 90.00 100.00 70
histological_type:
biphasic mesothelioma diffuse malignant mesothelioma - nos
23 5
epithelioid mesothelioma sarcomatoid mesothelioma
57 2
residual_tumor:
r0 r1 r2 rx NA's
17 3 15 11 41
race:
asian black or african american white
1 1 85
ethnicity:
not hispanic or latino NA's
73 14
Including an additional 636 columns
A document describing the TCGA cancer code
> experiments( MESO )
ExperimentList class object of length 10:
[1] MESO_CNASNP-20160128: RaggedExperiment with 90003 rows and 173 columns
[2] MESO_CNVSNP-20160128: RaggedExperiment with 18335 rows and 172 columns
[3] MESO_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[4] MESO_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 87 columns
[5] MESO_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[6] MESO_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 87 columns
[7] MESO_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[8] MESO_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 87 columns
[9] MESO_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18192 rows and 87 columns
[10] MESO_Methylation-20160128: SummarizedExperiment with 485577 rows and 87 columns
> rownames( MESO )
CharacterList of length 10
[["MESO_CNASNP-20160128"]] character(0)
[["MESO_CNVSNP-20160128"]] character(0)
[["MESO_GISTIC_AllByGene-20160128"]] character(0)
[["MESO_GISTIC_Peaks-20160128"]] 1 2 3 4 5 6 7 8 ... 14 15 16 17 18 19 20 21
[["MESO_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["MESO_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["MESO_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["MESO_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
[["MESO_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( MESO )
CharacterList of length 10
[["MESO_CNASNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_CNVSNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_AllByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_Peaks-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_ThresholdedByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_RNASeq2Gene-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RPPAArray-20160128"]] TCGA-3H-AB3K-01A-21-A45O-20 ...
[["MESO_miRNASeqGene-20160128"]] TCGA-3H-AB3K-01A-11R-A404-13 ...
[["MESO_RNASeq2GeneNorm-20160128"]] TCGA-3H-AB3K-01 ... TCGA-ZN-A9VW-01
[["MESO_Methylation-20160128"]] TCGA-3H-AB3K-01A-11D-A39S-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 MESO_CNASNP-20160128 2.5 Mb
2 MESO_CNVSNP-20160128 0.6 Mb
3 MESO_GISTIC_AllByGene-20160128 19.9 Mb
4 MESO_GISTIC_Peaks-20160128 0.1 Mb
5 MESO_GISTIC_ThresholdedByGene-20160128 19.8 Mb
6 MESO_RNASeq2Gene-20160128 16.2 Mb
7 MESO_RPPAArray-20160128 0.1 Mb
8 MESO_miRNASeqGene-20160128 0.9 Mb
9 MESO_RNASeq2GeneNorm-20160128 14.3 Mb
10 MESO_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
14 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 73 73 1.25 1.11 1.67
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 57.00 64.00 62.99 69.00 81.00
vital_status:
0 1
13 74
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 253.0 457.0 584.1 789.0 2790.0 14
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-8 499 1168 1091 1490 2359 74
tumor_tissue_site:
pleura
87
pathology_N_stage:
n0 n1 n2 n3 nx
44 10 26 3 4
pathology_M_stage:
m0 m1 mx
57 3 27
gender:
female male
16 71
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2008 2010 2009 2012 2013
radiation_therapy:
no yes NA's
62 24 1
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 77.65 90.00 100.00 70
histological_type:
biphasic mesothelioma diffuse malignant mesothelioma - nos
23 5
epithelioid mesothelioma sarcomatoid mesothelioma
57 2
residual_tumor:
r0 r1 r2 rx NA's
17 3 15 11 41
race:
asian black or african american white
1 1 85
ethnicity:
not hispanic or latino NA's
73 14
Including an additional 636 columns
A document describing the TCGA cancer code
> experiments( OV )
ExperimentList class object of length 19:
[1] OV_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 128946 rows and 472 columns
[2] OV_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 245847 rows and 674 columns
[3] OV_CNASNP-20160128: RaggedExperiment with 907765 rows and 1145 columns
[4] OV_CNVSNP-20160128: RaggedExperiment with 261680 rows and 1141 columns
[5] OV_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[6] OV_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 573 columns
[7] OV_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[8] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns
[9] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns
[10] OV_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 575 columns
[11] OV_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 577 columns
[12] OV_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 524 columns
[13] OV_Mutation-20160128: RaggedExperiment with 20219 rows and 316 columns
[14] OV_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 307 columns
[15] OV_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 307 columns
[16] OV_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 299 columns
[17] OV_RPPAArray-20160128: SummarizedExperiment with 208 rows and 427 columns
[18] OV_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 591 columns
[19] OV_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 10 columns
> rownames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["OV_CNASNP-20160128"]] character(0)
[["OV_CNVSNP-20160128"]] character(0)
[["OV_GISTIC_AllByGene-20160128"]] character(0)
[["OV_GISTIC_Peaks-20160128"]] 34 1 2 35 3 36 4 37 ... 70 28 29 30 71 31 72
[["OV_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["OV_miRNAArray-20160128"]] DarkCorner dmr_285 ... NegativeControl SCorner3
[["OV_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["OV_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
...
<9 more elements>
> colnames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] TCGA-04-1331-01A-01D-0431-02 ...
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-04-1353-01A-01D-1046-02 ...
[["OV_CNASNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_CNVSNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_AllByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_Peaks-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_ThresholdedByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_miRNAArray-20160128"]] TCGA-04-1331-01A-01T-0438-07 ...
[["OV_miRNASeqGene-20160128"]] TCGA-04-1331-01A-01R-1569-13 ...
[["OV_mRNAArray_huex-20160128"]] TCGA-04-1331-01A-01R-0435-03 ...
...
<9 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 OV_CNACGH_CGH_hg_244a-20160128 3.6 Mb
2 OV_CNACGH_CGH_hg_415k_g4124a-20160128 6.8 Mb
3 OV_CNASNP-20160128 24.6 Mb
4 OV_CNVSNP-20160128 7.3 Mb
5 OV_GISTIC_AllByGene-20160128 112 Mb
6 OV_GISTIC_Peaks-20160128 0.5 Mb
7 OV_GISTIC_ThresholdedByGene-20160128 111.7 Mb
8 OV_miRNAArray-20160128 3.8 Mb
9 OV_miRNASeqGene-20160128 2.7 Mb
10 OV_mRNAArray_huex-20160128 84.2 Mb
11 OV_mRNAArray_TX_g4502a-20160128 80.7 Mb
12 OV_mRNAArray_TX_ht_hg_u133a-20160128 49.7 Mb
13 OV_Mutation-20160128 10.3 Mb
14 OV_RNASeq2Gene-20160128 50.6 Mb
15 OV_RNASeq2GeneNorm-20160128 50.6 Mb
16 OV_RNASeqGene-20160128 48.1 Mb
17 OV_RPPAArray-20160128 0.8 Mb
18 OV_Methylation_methyl27-20160128 4.9 Mb
19 OV_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
343.00 343.00 2.94 2.76 3.17
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.78 69.00 89.00 21
vital_status:
0 1
246 344
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 567.5 1073.0 1147.4 1557.0 4624.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16 266 842 1216 1931 5481 358
tumor_tissue_site:
omentum ovary peritoneum ovary NA's
3 575 2 10
gender:
female NA's
580 10
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2001 2004 2004 2007 2013 10
radiation_therapy:
no yes NA's
556 5 29
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 60.00 80.00 75.83 80.00 100.00 506
histological_type:
serous cystadenocarcinoma NA's
580 10
residual_tumor:
r0 r1 r2 rx NA's
15 31 5 3 536
ethnicity:
hispanic or latino not hispanic or latino NA's
11 338 241
Including an additional 2869 columns
A document describing the TCGA cancer code
> experiments( OV )
ExperimentList class object of length 19:
[1] OV_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 128946 rows and 472 columns
[2] OV_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 245847 rows and 674 columns
[3] OV_CNASNP-20160128: RaggedExperiment with 907765 rows and 1145 columns
[4] OV_CNVSNP-20160128: RaggedExperiment with 261680 rows and 1141 columns
[5] OV_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[6] OV_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 573 columns
[7] OV_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[8] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns
[9] OV_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 575 columns
[10] OV_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 577 columns
[11] OV_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 524 columns
[12] OV_Mutation-20160128: RaggedExperiment with 20219 rows and 316 columns
[13] OV_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 307 columns
[14] OV_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 299 columns
[15] OV_RPPAArray-20160128: SummarizedExperiment with 208 rows and 427 columns
[16] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns
[17] OV_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18571 rows and 307 columns
[18] OV_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 591 columns
[19] OV_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 10 columns
> rownames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["OV_CNASNP-20160128"]] character(0)
[["OV_CNVSNP-20160128"]] character(0)
[["OV_GISTIC_AllByGene-20160128"]] character(0)
[["OV_GISTIC_Peaks-20160128"]] 34 1 2 35 3 36 4 37 ... 70 28 29 30 71 31 72
[["OV_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["OV_miRNAArray-20160128"]] DarkCorner dmr_285 ... NegativeControl SCorner3
[["OV_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["OV_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
...
<9 more elements>
> colnames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] TCGA-04-1331-01A-01D-0431-02 ...
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-04-1353-01A-01D-1046-02 ...
[["OV_CNASNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_CNVSNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_AllByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_Peaks-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_ThresholdedByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_miRNAArray-20160128"]] TCGA-04-1331-01A-01T-0438-07 ...
[["OV_mRNAArray_huex-20160128"]] TCGA-04-1331-01A-01R-0435-03 ...
[["OV_mRNAArray_TX_g4502a-20160128"]] TCGA-09-0364-01A-02R-0363-07 ...
...
<9 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 OV_CNACGH_CGH_hg_244a-20160128 3.6 Mb
2 OV_CNACGH_CGH_hg_415k_g4124a-20160128 6.8 Mb
3 OV_CNASNP-20160128 24.6 Mb
4 OV_CNVSNP-20160128 7.3 Mb
5 OV_GISTIC_AllByGene-20160128 112 Mb
6 OV_GISTIC_Peaks-20160128 0.5 Mb
7 OV_GISTIC_ThresholdedByGene-20160128 111.7 Mb
8 OV_miRNAArray-20160128 3.8 Mb
9 OV_mRNAArray_huex-20160128 84.2 Mb
10 OV_mRNAArray_TX_g4502a-20160128 80.7 Mb
11 OV_mRNAArray_TX_ht_hg_u133a-20160128 49.7 Mb
12 OV_Mutation-20160128 10.3 Mb
13 OV_RNASeq2Gene-20160128 50.6 Mb
14 OV_RNASeqGene-20160128 48.1 Mb
15 OV_RPPAArray-20160128 0.8 Mb
16 OV_miRNASeqGene-20160128 2.7 Mb
17 OV_RNASeq2GeneNorm-20160128 45.8 Mb
18 OV_Methylation_methyl27-20160128 4.9 Mb
19 OV_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 343 343 2.94 2.76 3.17
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.78 69.00 89.00 21
vital_status:
0 1
246 344
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 567.5 1073.0 1147.4 1557.0 4624.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16 266 842 1216 1931 5481 358
tumor_tissue_site:
omentum ovary peritoneum ovary NA's
3 575 2 10
gender:
female NA's
580 10
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2001 2004 2004 2007 2013 10
radiation_therapy:
no yes NA's
556 5 29
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 60.00 80.00 75.83 80.00 100.00 506
histological_type:
serous cystadenocarcinoma NA's
580 10
residual_tumor:
r0 r1 r2 rx NA's
15 31 5 3 536
ethnicity:
hispanic or latino not hispanic or latino NA's
11 338 241
Including an additional 2869 columns
A document describing the TCGA cancer code
Note. Only the colData has changed.
> experiments( OV )
ExperimentList class object of length 0:
> rownames( OV )
CharacterList of length 0
> colnames( OV )
CharacterList of length 0
Sizes of each ExperimentList element:
[1] assay size.Mb
<0 rows> (or 0-length row.names)
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
249 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 343 343 2.94 2.76 3.17
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.78 68.75 89.00 22
vital_status:
0 1 NA's
247 344 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 567.5 1073.0 1147.4 1557.0 4624.0 249
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16 268 837 1214 1919 5481 359
tumor_tissue_site:
omentum ovary peritoneum ovary NA's
3 576 2 11
gender:
female NA's
581 11
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2001 2004 2004 2007 2013 11
radiation_therapy:
no yes NA's
557 5 30
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 60.00 80.00 75.83 80.00 100.00 508
histological_type:
serous cystadenocarcinoma NA's
581 11
residual_tumor:
r0 r1 r2 rx NA's
16 31 5 3 537
ethnicity:
hispanic or latino not hispanic or latino NA's
11 338 243
Including an additional 2850 columns
A document describing the TCGA cancer code
> experiments( PAAD )
ExperimentList class object of length 11:
[1] PAAD_CNASNP-20160128: RaggedExperiment with 203871 rows and 368 columns
[2] PAAD_CNVSNP-20160128: RaggedExperiment with 34808 rows and 365 columns
[3] PAAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[4] PAAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 52 rows and 184 columns
[5] PAAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[6] PAAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 183 columns
[7] PAAD_Mutation-20160128: RaggedExperiment with 30357 rows and 150 columns
[8] PAAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 183 columns
[9] PAAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 183 columns
[10] PAAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 123 columns
[11] PAAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 195 columns
> rownames( PAAD )
CharacterList of length 11
[["PAAD_CNASNP-20160128"]] character(0)
[["PAAD_CNVSNP-20160128"]] character(0)
[["PAAD_GISTIC_AllByGene-20160128"]] character(0)
[["PAAD_GISTIC_Peaks-20160128"]] 24 1 2 3 25 4 26 5 ... 49 50 21 51 22 52 53
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PAAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PAAD_Mutation-20160128"]] character(0)
[["PAAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PAAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PAAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( PAAD )
CharacterList of length 11
[["PAAD_CNASNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_CNVSNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_AllByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_Peaks-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_miRNASeqGene-20160128"]] TCGA-2J-AAB1-01A-11R-A41G-13 ...
[["PAAD_Mutation-20160128"]] TCGA-2J-AAB1-01A-11D-A40W-08 ...
[["PAAD_RNASeq2Gene-20160128"]] TCGA-2J-AAB1-01A-11R-A41B-07 ...
[["PAAD_RNASeq2GeneNorm-20160128"]] TCGA-2J-AAB1-01A-11R-A41B-07 ...
[["PAAD_RPPAArray-20160128"]] TCGA-2J-AAB4-01A-21-A43K-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 PAAD_CNASNP-20160128 5.6 Mb
2 PAAD_CNVSNP-20160128 1 Mb
3 PAAD_GISTIC_AllByGene-20160128 38.3 Mb
4 PAAD_GISTIC_Peaks-20160128 0.2 Mb
5 PAAD_GISTIC_ThresholdedByGene-20160128 38.1 Mb
6 PAAD_miRNASeqGene-20160128 1.6 Mb
7 PAAD_Mutation-20160128 111 Mb
8 PAAD_RNASeq2Gene-20160128 31.2 Mb
9 PAAD_RNASeq2GeneNorm-20160128 31.2 Mb
10 PAAD_RPPAArray-20160128 0.2 Mb
11 PAAD_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
85 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
100.000 100.000 1.079 0.967 1.315
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
35.00 57.00 65.00 64.86 73.00 88.00
vital_status:
0 1
85 100
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
12.0 228.5 394.0 459.5 596.5 2182.0 85
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 338.0 517.0 692.4 951.0 2741.0 100
tumor_tissue_site:
pancreas
185
pathology_N_stage:
n0 n1 n1b nx NA's
50 126 4 4 1
pathology_M_stage:
m0 m1 mx
85 5 95
gender:
female male
83 102
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2001 2010 2012 2011 2012 2013 1
radiation_therapy:
no yes NA's
125 45 15
histological_type:
pancreas-adenocarcinoma ductal type
154
pancreas-adenocarcinoma-other subtype
25
pancreas-colloid (mucinous non-cystic) carcinoma
4
pancreas-undifferentiated carcinoma
1
NA's
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.30 15.00 25.00 26.84 40.00 75.00 128
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1948 1960 1971 1971 1982 1993 138
residual_tumor:
r0 r1 r2 rx NA's
111 53 5 4 12
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 2.000 2.989 4.000 16.000 4
race:
asian black or african american white
11 7 162
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
5 137 43
Including an additional 960 columns
A document describing the TCGA cancer code
> experiments( PAAD )
ExperimentList class object of length 11:
[1] PAAD_CNASNP-20160128: RaggedExperiment with 203871 rows and 368 columns
[2] PAAD_CNVSNP-20160128: RaggedExperiment with 34808 rows and 365 columns
[3] PAAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[4] PAAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 52 rows and 184 columns
[5] PAAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[6] PAAD_Mutation-20160128: RaggedExperiment with 30357 rows and 150 columns
[7] PAAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 183 columns
[8] PAAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 123 columns
[9] PAAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 183 columns
[10] PAAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18465 rows and 183 columns
[11] PAAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 195 columns
> rownames( PAAD )
CharacterList of length 11
[["PAAD_CNASNP-20160128"]] character(0)
[["PAAD_CNVSNP-20160128"]] character(0)
[["PAAD_GISTIC_AllByGene-20160128"]] character(0)
[["PAAD_GISTIC_Peaks-20160128"]] 24 1 2 3 25 4 26 5 ... 49 50 21 51 22 52 53
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PAAD_Mutation-20160128"]] character(0)
[["PAAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PAAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PAAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PAAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( PAAD )
CharacterList of length 11
[["PAAD_CNASNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_CNVSNP-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_AllByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_Peaks-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2J-AAB1-01A-11D-A40V-01 ...
[["PAAD_Mutation-20160128"]] TCGA-2J-AAB1-01A-11D-A40W-08 ...
[["PAAD_RNASeq2Gene-20160128"]] TCGA-2J-AAB1-01A-11R-A41B-07 ...
[["PAAD_RPPAArray-20160128"]] TCGA-2J-AAB4-01A-21-A43K-20 ...
[["PAAD_miRNASeqGene-20160128"]] TCGA-2J-AAB1-01A-11R-A41G-13 ...
[["PAAD_RNASeq2GeneNorm-20160128"]] TCGA-2J-AAB1-01 ... TCGA-Z5-AAPL-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 PAAD_CNASNP-20160128 5.6 Mb
2 PAAD_CNVSNP-20160128 1 Mb
3 PAAD_GISTIC_AllByGene-20160128 38.3 Mb
4 PAAD_GISTIC_Peaks-20160128 0.2 Mb
5 PAAD_GISTIC_ThresholdedByGene-20160128 38.1 Mb
6 PAAD_Mutation-20160128 111 Mb
7 PAAD_RNASeq2Gene-20160128 31.2 Mb
8 PAAD_RPPAArray-20160128 0.2 Mb
9 PAAD_miRNASeqGene-20160128 1.6 Mb
10 PAAD_RNASeq2GeneNorm-20160128 28.1 Mb
11 PAAD_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
85 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 100 100 1.08 0.967 1.32
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
35.00 57.00 65.00 64.86 73.00 88.00
vital_status:
0 1
85 100
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
12.0 228.5 394.0 459.5 596.5 2182.0 85
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 338.0 517.0 692.4 951.0 2741.0 100
tumor_tissue_site:
pancreas
185
pathology_N_stage:
n0 n1 n1b nx NA's
50 126 4 4 1
pathology_M_stage:
m0 m1 mx
85 5 95
gender:
female male
83 102
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2001 2010 2012 2011 2012 2013 1
radiation_therapy:
no yes NA's
125 45 15
histological_type:
pancreas-adenocarcinoma ductal type
154
pancreas-adenocarcinoma-other subtype
25
pancreas-colloid (mucinous non-cystic) carcinoma
4
pancreas-undifferentiated carcinoma
1
NA's
1
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.30 15.00 25.00 26.84 40.00 75.00 128
year_of_tobacco_smoking_onset:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1948 1960 1971 1971 1982 1993 138
residual_tumor:
r0 r1 r2 rx NA's
111 53 5 4 12
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 2.000 2.989 4.000 16.000 4
race:
asian black or african american white
11 7 162
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
5 137 43
Including an additional 960 columns
A document describing the TCGA cancer code
> experiments( PCPG )
ExperimentList class object of length 11:
[1] PCPG_CNASNP-20160128: RaggedExperiment with 297329 rows and 360 columns
[2] PCPG_CNVSNP-20160128: RaggedExperiment with 31256 rows and 346 columns
[3] PCPG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[4] PCPG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 27 rows and 162 columns
[5] PCPG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[6] PCPG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 187 columns
[7] PCPG_Mutation-20160128: RaggedExperiment with 4662 rows and 184 columns
[8] PCPG_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 187 columns
[9] PCPG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 187 columns
[10] PCPG_RPPAArray-20160128: SummarizedExperiment with 192 rows and 82 columns
[11] PCPG_Methylation-20160128: SummarizedExperiment with 485577 rows and 187 columns
> rownames( PCPG )
CharacterList of length 11
[["PCPG_CNASNP-20160128"]] character(0)
[["PCPG_CNVSNP-20160128"]] character(0)
[["PCPG_GISTIC_AllByGene-20160128"]] character(0)
[["PCPG_GISTIC_Peaks-20160128"]] 7 1 8 9 10 11 2 12 ... 22 23 5 24 25 26 6 27
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PCPG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PCPG_Mutation-20160128"]] character(0)
[["PCPG_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PCPG_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["PCPG_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( PCPG )
CharacterList of length 11
[["PCPG_CNASNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_CNVSNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_GISTIC_AllByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_Peaks-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_miRNASeqGene-20160128"]] TCGA-P7-A5NX-01A-11R-A35M-13 ...
[["PCPG_Mutation-20160128"]] TCGA-P7-A5NX-01A-11D-A35D-08 ...
[["PCPG_RNASeq2Gene-20160128"]] TCGA-P7-A5NX-01A-11R-A35K-07 ...
[["PCPG_RNASeq2GeneNorm-20160128"]] TCGA-P7-A5NX-01A-11R-A35K-07 ...
[["PCPG_RPPAArray-20160128"]] TCGA-P7-A5NX-01A-21-A43B-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 PCPG_CNASNP-20160128 8.1 Mb
2 PCPG_CNVSNP-20160128 0.9 Mb
3 PCPG_GISTIC_AllByGene-20160128 34.1 Mb
4 PCPG_GISTIC_Peaks-20160128 0.1 Mb
5 PCPG_GISTIC_ThresholdedByGene-20160128 34 Mb
6 PCPG_miRNASeqGene-20160128 1.7 Mb
7 PCPG_Mutation-20160128 8.4 Mb
8 PCPG_RNASeq2Gene-20160128 31.8 Mb
9 PCPG_RNASeq2GeneNorm-20160128 31.8 Mb
10 PCPG_RPPAArray-20160128 0.2 Mb
11 PCPG_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
173 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
6.00 6.00 1.24 0.26 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
19.00 35.00 46.00 47.33 58.50 83.00
vital_status:
0 1
173 6
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
88.0 148.5 452.5 901.0 715.2 3563.0 173
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2 352 766 1071 1301 9634 6
tumor_tissue_site:
adrenal gland extra-adrenal site
147 32
gender:
female male
101 78
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1988 2009 2011 2010 2012 2013
radiation_therapy:
no yes NA's
172 5 2
karnofsky_performance_score:
70 80 90 100 NA's
1 2 13 46 117
histological_type:
paraganglioma
18
paraganglioma; extra-adrenal pheochromocytoma
13
pheochromocytoma
148
number_of_lymph_nodes:
0 1 2 13 NA's
16 3 1 1 158
race:
american indian or alaska native asian
1 6
black or african american white
20 148
NA's
4
ethnicity:
hispanic or latino not hispanic or latino NA's
5 138 36
Including an additional 894 columns
A document describing the TCGA cancer code
> experiments( PCPG )
ExperimentList class object of length 11:
[1] PCPG_CNASNP-20160128: RaggedExperiment with 297329 rows and 360 columns
[2] PCPG_CNVSNP-20160128: RaggedExperiment with 31256 rows and 346 columns
[3] PCPG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[4] PCPG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 27 rows and 162 columns
[5] PCPG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns
[6] PCPG_Mutation-20160128: RaggedExperiment with 4662 rows and 184 columns
[7] PCPG_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 187 columns
[8] PCPG_RPPAArray-20160128: SummarizedExperiment with 192 rows and 82 columns
[9] PCPG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 187 columns
[10] PCPG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17988 rows and 187 columns
[11] PCPG_Methylation-20160128: SummarizedExperiment with 485577 rows and 187 columns
> rownames( PCPG )
CharacterList of length 11
[["PCPG_CNASNP-20160128"]] character(0)
[["PCPG_CNVSNP-20160128"]] character(0)
[["PCPG_GISTIC_AllByGene-20160128"]] character(0)
[["PCPG_GISTIC_Peaks-20160128"]] 7 1 8 9 10 11 2 12 ... 22 23 5 24 25 26 6 27
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PCPG_Mutation-20160128"]] character(0)
[["PCPG_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PCPG_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PCPG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PCPG_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( PCPG )
CharacterList of length 11
[["PCPG_CNASNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_CNVSNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ...
[["PCPG_GISTIC_AllByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_Peaks-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_GISTIC_ThresholdedByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ...
[["PCPG_Mutation-20160128"]] TCGA-P7-A5NX-01A-11D-A35D-08 ...
[["PCPG_RNASeq2Gene-20160128"]] TCGA-P7-A5NX-01A-11R-A35K-07 ...
[["PCPG_RPPAArray-20160128"]] TCGA-P7-A5NX-01A-21-A43B-20 ...
[["PCPG_miRNASeqGene-20160128"]] TCGA-P7-A5NX-01A-11R-A35M-13 ...
[["PCPG_RNASeq2GeneNorm-20160128"]] TCGA-P7-A5NX-01 ... TCGA-XG-A823-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 PCPG_CNASNP-20160128 8.1 Mb
2 PCPG_CNVSNP-20160128 0.9 Mb
3 PCPG_GISTIC_AllByGene-20160128 34.1 Mb
4 PCPG_GISTIC_Peaks-20160128 0.1 Mb
5 PCPG_GISTIC_ThresholdedByGene-20160128 34 Mb
6 PCPG_Mutation-20160128 8.4 Mb
7 PCPG_RNASeq2Gene-20160128 31.8 Mb
8 PCPG_RPPAArray-20160128 0.2 Mb
9 PCPG_miRNASeqGene-20160128 1.7 Mb
10 PCPG_RNASeq2GeneNorm-20160128 27.9 Mb
11 PCPG_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
173 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 6 6 1.24 0.26 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
19.00 35.00 46.00 47.33 58.50 83.00
vital_status:
0 1
173 6
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
88.0 148.5 452.5 901.0 715.2 3563.0 173
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2 352 766 1071 1301 9634 6
tumor_tissue_site:
adrenal gland extra-adrenal site
147 32
gender:
female male
101 78
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1988 2009 2011 2010 2012 2013
radiation_therapy:
no yes NA's
172 5 2
karnofsky_performance_score:
70 80 90 100 NA's
1 2 13 46 117
histological_type:
paraganglioma
18
paraganglioma; extra-adrenal pheochromocytoma
13
pheochromocytoma
148
number_of_lymph_nodes:
0 1 2 13 NA's
16 3 1 1 158
race:
american indian or alaska native asian
1 6
black or african american white
20 148
NA's
4
ethnicity:
hispanic or latino not hispanic or latino NA's
5 138 36
Including an additional 894 columns
A document describing the TCGA cancer code
> experiments( PRAD )
ExperimentList class object of length 12:
[1] PRAD_CNASeq-20160128: RaggedExperiment with 23398 rows and 230 columns
[2] PRAD_CNASNP-20160128: RaggedExperiment with 573776 rows and 1029 columns
[3] PRAD_CNVSNP-20160128: RaggedExperiment with 117345 rows and 1023 columns
[4] PRAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[5] PRAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 58 rows and 492 columns
[6] PRAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[7] PRAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 547 columns
[8] PRAD_Mutation-20160128: RaggedExperiment with 12348 rows and 332 columns
[9] PRAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 550 columns
[10] PRAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 550 columns
[11] PRAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 352 columns
[12] PRAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 549 columns
> rownames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] character(0)
[["PRAD_CNASNP-20160128"]] character(0)
[["PRAD_CNVSNP-20160128"]] character(0)
[["PRAD_GISTIC_AllByGene-20160128"]] character(0)
[["PRAD_GISTIC_Peaks-20160128"]] 29 30 1 31 32 33 34 ... 21 60 61 22 23 62 63
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PRAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["PRAD_Mutation-20160128"]] character(0)
[["PRAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PRAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] TCGA-CH-5741-01A-11D-1572-02 ...
[["PRAD_CNASNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_CNVSNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_AllByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_Peaks-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_miRNASeqGene-20160128"]] TCGA-2A-A8VL-01A-21R-A37H-13 ...
[["PRAD_Mutation-20160128"]] TCGA-2A-A8VL-01A-21D-A377-08 ...
[["PRAD_RNASeq2Gene-20160128"]] TCGA-2A-A8VL-01A-21R-A37L-07 ...
[["PRAD_RNASeq2GeneNorm-20160128"]] TCGA-2A-A8VL-01A-21R-A37L-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 PRAD_CNASeq-20160128 0.7 Mb
2 PRAD_CNASNP-20160128 15.6 Mb
3 PRAD_CNVSNP-20160128 3.4 Mb
4 PRAD_GISTIC_AllByGene-20160128 96.6 Mb
5 PRAD_GISTIC_Peaks-20160128 0.4 Mb
6 PRAD_GISTIC_ThresholdedByGene-20160128 96.4 Mb
7 PRAD_miRNASeqGene-20160128 4.6 Mb
8 PRAD_Mutation-20160128 21.5 Mb
9 PRAD_RNASeq2Gene-20160128 88.7 Mb
10 PRAD_RNASeq2GeneNorm-20160128 88.7 Mb
11 PRAD_RPPAArray-20160128 0.6 Mb
12 PRAD_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
488 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
10.00 10.00 3.02 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
41.00 56.00 61.00 61.02 66.00 78.00 11
vital_status:
0 1
488 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
146.0 743.8 1102.0 1579.0 2315.5 3502.0 488
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
23.0 523.5 926.0 1076.5 1458.0 5024.0 10
tumor_tissue_site:
prostate
498
pathology_N_stage:
n0 n1 NA's
346 79 73
gender:
male
498
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2009 2011 2010 2012 2013 31
radiation_therapy:
no yes NA's
395 59 44
histological_type:
prostate adenocarcinoma acinar type prostate adenocarcinoma, other subtype
483 15
residual_tumor:
r0 r1 r2 rx NA's
316 147 5 15 15
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.4447 0.0000 15.0000 91
gleason_score:
6 7 8 9 10
45 248 64 137 4
psa_value:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.030 0.100 1.742 0.110 323.000 57
days_to_psa:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-164.0 191.0 512.0 685.6 926.0 3447.0 53
race:
asian black or african american white
2 7 147
NA's
342
ethnicity:
not hispanic or latino NA's
152 346
Including an additional 1126 columns
A document describing the TCGA cancer code
> experiments( PRAD )
ExperimentList class object of length 12:
[1] PRAD_CNASeq-20160128: RaggedExperiment with 23398 rows and 230 columns
[2] PRAD_CNASNP-20160128: RaggedExperiment with 573776 rows and 1029 columns
[3] PRAD_CNVSNP-20160128: RaggedExperiment with 117345 rows and 1023 columns
[4] PRAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[5] PRAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 58 rows and 492 columns
[6] PRAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[7] PRAD_Mutation-20160128: RaggedExperiment with 12348 rows and 332 columns
[8] PRAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 550 columns
[9] PRAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 352 columns
[10] PRAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 547 columns
[11] PRAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18265 rows and 550 columns
[12] PRAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 549 columns
> rownames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] character(0)
[["PRAD_CNASNP-20160128"]] character(0)
[["PRAD_CNVSNP-20160128"]] character(0)
[["PRAD_GISTIC_AllByGene-20160128"]] character(0)
[["PRAD_GISTIC_Peaks-20160128"]] 29 30 1 31 32 33 34 ... 21 60 61 22 23 62 63
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PRAD_Mutation-20160128"]] character(0)
[["PRAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PRAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PRAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] TCGA-CH-5741-01A-11D-1572-02 ...
[["PRAD_CNASNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_CNVSNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_AllByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_Peaks-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_Mutation-20160128"]] TCGA-2A-A8VL-01A-21D-A377-08 ...
[["PRAD_RNASeq2Gene-20160128"]] TCGA-2A-A8VL-01A-21R-A37L-07 ...
[["PRAD_RPPAArray-20160128"]] TCGA-2A-A8VL-01A-11-A43M-20 ...
[["PRAD_miRNASeqGene-20160128"]] TCGA-2A-A8VL-01A-21R-A37H-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 PRAD_CNASeq-20160128 0.7 Mb
2 PRAD_CNASNP-20160128 15.6 Mb
3 PRAD_CNVSNP-20160128 3.4 Mb
4 PRAD_GISTIC_AllByGene-20160128 96.6 Mb
5 PRAD_GISTIC_Peaks-20160128 0.4 Mb
6 PRAD_GISTIC_ThresholdedByGene-20160128 96.4 Mb
7 PRAD_Mutation-20160128 21.5 Mb
8 PRAD_RNASeq2Gene-20160128 88.7 Mb
9 PRAD_RPPAArray-20160128 0.6 Mb
10 PRAD_miRNASeqGene-20160128 4.6 Mb
11 PRAD_RNASeq2GeneNorm-20160128 79 Mb
12 PRAD_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
488 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 10 10 3.02 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
41.00 56.00 61.00 61.02 66.00 78.00 11
vital_status:
0 1
488 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
146.0 743.8 1102.0 1579.0 2315.5 3502.0 488
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
23.0 523.5 926.0 1076.5 1458.0 5024.0 10
tumor_tissue_site:
prostate
498
pathology_N_stage:
n0 n1 NA's
346 79 73
gender:
male
498
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2009 2011 2010 2012 2013 31
radiation_therapy:
no yes NA's
395 59 44
histological_type:
prostate adenocarcinoma acinar type prostate adenocarcinoma, other subtype
483 15
residual_tumor:
r0 r1 r2 rx NA's
316 147 5 15 15
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.4447 0.0000 15.0000 91
gleason_score:
6 7 8 9 10
45 248 64 137 4
psa_value:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.030 0.100 1.742 0.110 323.000 57
days_to_psa:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-164.0 191.0 512.0 685.6 926.0 3447.0 53
race:
asian black or african american white
2 7 147
NA's
342
ethnicity:
not hispanic or latino NA's
152 346
Including an additional 1126 columns
A document describing the TCGA cancer code
> experiments( READ )
ExperimentList class object of length 16:
[1] READ_CNASeq-20160128: RaggedExperiment with 56380 rows and 70 columns
[2] READ_CNASNP-20160128: RaggedExperiment with 156806 rows and 316 columns
[3] READ_CNVSNP-20160128: RaggedExperiment with 35765 rows and 316 columns
[4] READ_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[5] READ_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 55 rows and 165 columns
[6] READ_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[7] READ_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 76 columns
[8] READ_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[9] READ_Mutation-20160128: RaggedExperiment with 22075 rows and 69 columns
[10] READ_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 105 columns
[11] READ_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 72 columns
[12] READ_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 105 columns
[13] READ_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 72 columns
[14] READ_RPPAArray-20160128: SummarizedExperiment with 208 rows and 131 columns
[15] READ_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[16] READ_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 106 columns
> rownames( READ )
CharacterList of length 16
[["READ_CNASeq-20160128"]] character(0)
[["READ_CNASNP-20160128"]] character(0)
[["READ_CNVSNP-20160128"]] character(0)
[["READ_GISTIC_AllByGene-20160128"]] character(0)
[["READ_GISTIC_Peaks-20160128"]] 23 24 25 1 2 26 27 ... 54 55 18 19 20 56 57
[["READ_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["READ_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["READ_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["READ_Mutation-20160128"]] character(0)
[["READ_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<6 more elements>
> colnames( READ )
CharacterList of length 16
[["READ_CNASeq-20160128"]] TCGA-AF-2691-01A-01D-1167-02 ...
[["READ_CNASNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_CNVSNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_AllByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_Peaks-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_ThresholdedByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_miRNASeqGene-20160128"]] TCGA-AF-2687-01A-02T-1735-13 ...
[["READ_mRNAArray-20160128"]] TCGA-AF-2689-11A-01R-1758-07 ...
[["READ_Mutation-20160128"]] TCGA-AF-2689-01A-01W-0831-10 ... TCGA-AG-A036-01
[["READ_RNASeq2Gene-20160128"]] TCGA-AF-2687-01A-02R-1736-07 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 READ_CNASeq-20160128 1.5 Mb
2 READ_CNASNP-20160128 4.3 Mb
3 READ_CNVSNP-20160128 1.1 Mb
4 READ_GISTIC_AllByGene-20160128 34.7 Mb
5 READ_GISTIC_Peaks-20160128 0.2 Mb
6 READ_GISTIC_ThresholdedByGene-20160128 34.5 Mb
7 READ_miRNASeqGene-20160128 0.5 Mb
8 READ_mRNAArray-20160128 12 Mb
9 READ_Mutation-20160128 9.6 Mb
10 READ_RNASeq2Gene-20160128 19 Mb
11 READ_RNASeq2GeneNorm_illuminaga-20160128 13.8 Mb
12 READ_RNASeq2GeneNorm_illuminahiseq-20160128 19 Mb
13 READ_RNASeqGene-20160128 13.8 Mb
14 READ_RPPAArray-20160128 0.3 Mb
15 READ_Methylation_methyl27-20160128 4.9 Mb
16 READ_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
142 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
27.00 27.00 2.00 1.44 3.25
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
31.00 57.00 66.00 64.37 72.00 90.00
vital_status:
0 1
141 28
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
59.0 347.5 730.0 786.1 1193.0 1741.0 142
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 366.0 625.0 779.5 1096.0 3932.0 28
tumor_tissue_site:
rectum NA's
166 3
pathology_M_stage:
m0 m1 m1a mx NA's
128 22 2 14 3
gender:
female male
77 92
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2007 2009 2008 2010 2012
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.0 292.2 863.0 1420.1 2214.5 3667.0 161
radiation_therapy:
no yes NA's
114 22 33
histological_type:
rectal adenocarcinoma rectal mucinous adenocarcinoma
150 13
NA's
6
tumor_stage:
stage iia NA's
1 168
residual_tumor:
r0 r1 r2 rx NA's
126 2 12 5 24
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.692 3.000 31.000 10
ethnicity:
hispanic or latino not hispanic or latino NA's
1 84 84
Including an additional 2242 columns
A document describing the TCGA cancer code
> experiments( READ )
ExperimentList class object of length 17:
[1] READ_CNASeq-20160128: RaggedExperiment with 56380 rows and 70 columns
[2] READ_CNASNP-20160128: RaggedExperiment with 156806 rows and 316 columns
[3] READ_CNVSNP-20160128: RaggedExperiment with 35765 rows and 316 columns
[4] READ_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[5] READ_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 55 rows and 165 columns
[6] READ_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 165 columns
[7] READ_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns
[8] READ_Mutation-20160128: RaggedExperiment with 22075 rows and 69 columns
[9] READ_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 105 columns
[10] READ_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 72 columns
[11] READ_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 105 columns
[12] READ_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 72 columns
[13] READ_RPPAArray-20160128: SummarizedExperiment with 208 rows and 131 columns
[14] READ_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 76 columns
[15] READ_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18115 rows and 177 columns
[16] READ_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[17] READ_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 106 columns
> rownames( READ )
CharacterList of length 17
[["READ_CNASeq-20160128"]] character(0)
[["READ_CNASNP-20160128"]] character(0)
[["READ_CNVSNP-20160128"]] character(0)
[["READ_GISTIC_AllByGene-20160128"]] character(0)
[["READ_GISTIC_Peaks-20160128"]] 23 24 25 1 2 26 27 ... 54 55 18 19 20 56 57
[["READ_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["READ_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["READ_Mutation-20160128"]] character(0)
[["READ_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["READ_RNASeq2GeneNorm_illuminaga-20160128"]] A1BG A1CF ... psiTPTE22 tAKR
...
<7 more elements>
> colnames( READ )
CharacterList of length 17
[["READ_CNASeq-20160128"]] TCGA-AF-2691-01A-01D-1167-02 ...
[["READ_CNASNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_CNVSNP-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_AllByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_Peaks-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_GISTIC_ThresholdedByGene-20160128"]] TCGA-AF-2687-01A-02D-1732-01 ...
[["READ_mRNAArray-20160128"]] TCGA-AF-2689-11A-01R-1758-07 ...
[["READ_Mutation-20160128"]] TCGA-AF-2689-01A-01W-0831-10 ... TCGA-AG-A036-01
[["READ_RNASeq2Gene-20160128"]] TCGA-AF-2687-01A-02R-1736-07 ...
[["READ_RNASeq2GeneNorm_illuminaga-20160128"]] TCGA-AF-2691-01A-01R-0821-07...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 READ_CNASeq-20160128 1.5 Mb
2 READ_CNASNP-20160128 4.3 Mb
3 READ_CNVSNP-20160128 1.1 Mb
4 READ_GISTIC_AllByGene-20160128 34.7 Mb
5 READ_GISTIC_Peaks-20160128 0.2 Mb
6 READ_GISTIC_ThresholdedByGene-20160128 34.5 Mb
7 READ_mRNAArray-20160128 12 Mb
8 READ_Mutation-20160128 9.6 Mb
9 READ_RNASeq2Gene-20160128 19 Mb
10 READ_RNASeq2GeneNorm_illuminaga-20160128 13.8 Mb
11 READ_RNASeq2GeneNorm_illuminahiseq-20160128 19 Mb
12 READ_RNASeqGene-20160128 13.8 Mb
13 READ_RPPAArray-20160128 0.3 Mb
14 READ_miRNASeqGene-20160128 0.5 Mb
15 READ_RNASeq2GeneNorm-20160128 26.7 Mb
16 READ_Methylation_methyl27-20160128 4.9 Mb
17 READ_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
142 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 27 27 2 1.44 3.25
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
31.00 57.00 66.00 64.37 72.00 90.00
vital_status:
0 1
141 28
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
59.0 347.5 730.0 786.1 1193.0 1741.0 142
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 366.0 625.0 779.5 1096.0 3932.0 28
tumor_tissue_site:
rectum NA's
166 3
pathology_M_stage:
m0 m1 m1a mx NA's
128 22 2 14 3
gender:
female male
77 92
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2007 2009 2008 2010 2012
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.0 292.2 863.0 1420.1 2214.5 3667.0 161
radiation_therapy:
no yes NA's
114 22 33
histological_type:
rectal adenocarcinoma rectal mucinous adenocarcinoma
150 13
NA's
6
tumor_stage:
stage iia NA's
1 168
residual_tumor:
r0 r1 r2 rx NA's
126 2 12 5 24
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.692 3.000 31.000 10
ethnicity:
hispanic or latino not hispanic or latino NA's
1 84 84
Including an additional 2242 columns
A document describing the TCGA cancer code
> experiments( SARC )
ExperimentList class object of length 11:
[1] SARC_CNASNP-20160128: RaggedExperiment with 337377 rows and 516 columns
[2] SARC_CNVSNP-20160128: RaggedExperiment with 106739 rows and 513 columns
[3] SARC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[4] SARC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 64 rows and 257 columns
[5] SARC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[6] SARC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 263 columns
[7] SARC_Mutation-20160128: RaggedExperiment with 20376 rows and 247 columns
[8] SARC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 265 columns
[9] SARC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 265 columns
[10] SARC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 226 columns
[11] SARC_Methylation-20160128: SummarizedExperiment with 485577 rows and 269 columns
> rownames( SARC )
CharacterList of length 11
[["SARC_CNASNP-20160128"]] character(0)
[["SARC_CNVSNP-20160128"]] character(0)
[["SARC_GISTIC_AllByGene-20160128"]] character(0)
[["SARC_GISTIC_Peaks-20160128"]] 26 1 2 3 27 28 4 29 ... 21 63 22 64 23 65 66
[["SARC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["SARC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SARC_Mutation-20160128"]] character(0)
[["SARC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["SARC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["SARC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( SARC )
CharacterList of length 11
[["SARC_CNASNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_CNVSNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_AllByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_Peaks-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_miRNASeqGene-20160128"]] TCGA-3B-A9HI-01A-11R-A38N-13 ...
[["SARC_Mutation-20160128"]] TCGA-3B-A9HI-01A-11D-A387-09 ...
[["SARC_RNASeq2Gene-20160128"]] TCGA-3B-A9HI-01A-11R-A38C-07 ...
[["SARC_RNASeq2GeneNorm-20160128"]] TCGA-3B-A9HI-01A-11R-A38C-07 ...
[["SARC_RPPAArray-20160128"]] TCGA-3B-A9HI-01A-21-A456-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 SARC_CNASNP-20160128 9.2 Mb
2 SARC_CNVSNP-20160128 3 Mb
3 SARC_GISTIC_AllByGene-20160128 52.2 Mb
4 SARC_GISTIC_Peaks-20160128 0.2 Mb
5 SARC_GISTIC_ThresholdedByGene-20160128 51.9 Mb
6 SARC_miRNASeqGene-20160128 2.3 Mb
7 SARC_Mutation-20160128 19.5 Mb
8 SARC_RNASeq2Gene-20160128 44 Mb
9 SARC_RNASeq2GeneNorm-20160128 44 Mb
10 SARC_RPPAArray-20160128 0.4 Mb
11 SARC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
162 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
99.00 99.00 1.78 1.51 2.46
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 53.00 61.00 60.88 71.00 90.00 1
vital_status:
0 1
162 99
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.0 322.5 648.0 863.6 1169.5 2694.0 162
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.0 585.8 1092.0 1391.1 1891.8 5723.0 99
gender:
female male
142 119
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2007 2010 2009 2012 2013 4
radiation_therapy:
no yes NA's
181 74 6
residual_tumor:
r0 r1 r2 rx NA's
155 70 9 26 1
race:
asian black or african american white
6 18 228
NA's
9
ethnicity:
hispanic or latino not hispanic or latino NA's
5 223 33
Including an additional 1413 columns
A document describing the TCGA cancer code
> experiments( SARC )
ExperimentList class object of length 11:
[1] SARC_CNASNP-20160128: RaggedExperiment with 337377 rows and 516 columns
[2] SARC_CNVSNP-20160128: RaggedExperiment with 106739 rows and 513 columns
[3] SARC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[4] SARC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 64 rows and 257 columns
[5] SARC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[6] SARC_Mutation-20160128: RaggedExperiment with 20376 rows and 247 columns
[7] SARC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 265 columns
[8] SARC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 226 columns
[9] SARC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 263 columns
[10] SARC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18165 rows and 265 columns
[11] SARC_Methylation-20160128: SummarizedExperiment with 485577 rows and 269 columns
> rownames( SARC )
CharacterList of length 11
[["SARC_CNASNP-20160128"]] character(0)
[["SARC_CNVSNP-20160128"]] character(0)
[["SARC_GISTIC_AllByGene-20160128"]] character(0)
[["SARC_GISTIC_Peaks-20160128"]] 26 1 2 3 27 28 4 29 ... 21 63 22 64 23 65 66
[["SARC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["SARC_Mutation-20160128"]] character(0)
[["SARC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["SARC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["SARC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SARC_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( SARC )
CharacterList of length 11
[["SARC_CNASNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_CNVSNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_AllByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_Peaks-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_Mutation-20160128"]] TCGA-3B-A9HI-01A-11D-A387-09 ...
[["SARC_RNASeq2Gene-20160128"]] TCGA-3B-A9HI-01A-11R-A38C-07 ...
[["SARC_RPPAArray-20160128"]] TCGA-3B-A9HI-01A-21-A456-20 ...
[["SARC_miRNASeqGene-20160128"]] TCGA-3B-A9HI-01A-11R-A38N-13 ...
[["SARC_RNASeq2GeneNorm-20160128"]] TCGA-3B-A9HI-01 ... TCGA-Z4-AAPG-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 SARC_CNASNP-20160128 9.2 Mb
2 SARC_CNVSNP-20160128 3 Mb
3 SARC_GISTIC_AllByGene-20160128 52.2 Mb
4 SARC_GISTIC_Peaks-20160128 0.2 Mb
5 SARC_GISTIC_ThresholdedByGene-20160128 51.9 Mb
6 SARC_Mutation-20160128 19.5 Mb
7 SARC_RNASeq2Gene-20160128 44 Mb
8 SARC_RPPAArray-20160128 0.4 Mb
9 SARC_miRNASeqGene-20160128 2.3 Mb
10 SARC_RNASeq2GeneNorm-20160128 39 Mb
11 SARC_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
162 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 99 99 1.78 1.51 2.46
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 53.00 61.00 60.88 71.00 90.00 1
vital_status:
0 1
162 99
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.0 322.5 648.0 863.6 1169.5 2694.0 162
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.0 585.8 1092.0 1391.1 1891.8 5723.0 99
gender:
female male
142 119
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2007 2010 2009 2012 2013 4
radiation_therapy:
no yes NA's
181 74 6
residual_tumor:
r0 r1 r2 rx NA's
155 70 9 26 1
race:
asian black or african american white
6 18 228
NA's
9
ethnicity:
hispanic or latino not hispanic or latino NA's
5 223 33
Including an additional 1413 columns
A document describing the TCGA cancer code
> experiments( SKCM )
ExperimentList class object of length 12:
[1] SKCM_CNASeq-20160128: RaggedExperiment with 31416 rows and 238 columns
[2] SKCM_CNASNP-20160128: RaggedExperiment with 452114 rows and 938 columns
[3] SKCM_CNVSNP-20160128: RaggedExperiment with 108084 rows and 937 columns
[4] SKCM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[5] SKCM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 53 rows and 367 columns
[6] SKCM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[7] SKCM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 452 columns
[8] SKCM_Mutation-20160128: RaggedExperiment with 290322 rows and 345 columns
[9] SKCM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 473 columns
[10] SKCM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 473 columns
[11] SKCM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 355 columns
[12] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns
> rownames( SKCM )
CharacterList of length 12
[["SKCM_CNASeq-20160128"]] character(0)
[["SKCM_CNASNP-20160128"]] character(0)
[["SKCM_CNVSNP-20160128"]] character(0)
[["SKCM_GISTIC_AllByGene-20160128"]] character(0)
[["SKCM_GISTIC_Peaks-20160128"]] 21 22 1 2 3 23 24 4 ... 50 51 52 18 53 19 20
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["SKCM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SKCM_Mutation-20160128"]] character(0)
[["SKCM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["SKCM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( SKCM )
CharacterList of length 12
[["SKCM_CNASeq-20160128"]] TCGA-BF-A1PU-01A-11D-A18Z-02 ...
[["SKCM_CNASNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_CNVSNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_AllByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_Peaks-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_miRNASeqGene-20160128"]] TCGA-3N-A9WC-06A-11R-A38N-13 ...
[["SKCM_Mutation-20160128"]] TCGA-BF-A1PU-01A-11D-A19A-08 ...
[["SKCM_RNASeq2Gene-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
[["SKCM_RNASeq2GeneNorm-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 SKCM_CNASeq-20160128 0.9 Mb
2 SKCM_CNASNP-20160128 12.3 Mb
3 SKCM_CNVSNP-20160128 3.2 Mb
4 SKCM_GISTIC_AllByGene-20160128 73 Mb
5 SKCM_GISTIC_Peaks-20160128 0.3 Mb
6 SKCM_GISTIC_ThresholdedByGene-20160128 72.8 Mb
7 SKCM_miRNASeqGene-20160128 3.8 Mb
8 SKCM_Mutation-20160128 299.6 Mb
9 SKCM_RNASeq2Gene-20160128 76.6 Mb
10 SKCM_RNASeq2GeneNorm-20160128 76.6 Mb
11 SKCM_RPPAArray-20160128 0.7 Mb
12 SKCM_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
249 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
221.00 221.00 2.99 2.40 3.90
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.00 48.00 58.00 58.24 71.00 90.00 8
vital_status:
0 1
247 223
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
79 518 1093 1789 2073 10870 249
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2.0 477.5 1146.0 1885.3 2658.8 11252.0 230
days_to_submitted_specimen_dx:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2 0 344 1017 1372 10847 14
melanoma_ulceration:
no yes NA's
146 167 157
melanoma_primary_known:
no yes
47 423
Breslow_thickness:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.300 3.000 5.585 6.950 75.000 111
gender:
female male
180 290
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1978 2003 2008 2006 2011 2013 11
radiation_therapy:
no yes NA's
420 49 1
race:
asian black or african american white
12 1 447
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
11 446 13
Including an additional 1517 columns
A document describing the TCGA cancer code
> experiments( SKCM )
ExperimentList class object of length 12:
[1] SKCM_CNASeq-20160128: RaggedExperiment with 31416 rows and 238 columns
[2] SKCM_CNASNP-20160128: RaggedExperiment with 452114 rows and 938 columns
[3] SKCM_CNVSNP-20160128: RaggedExperiment with 108084 rows and 937 columns
[4] SKCM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[5] SKCM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 53 rows and 367 columns
[6] SKCM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
[7] SKCM_Mutation-20160128: RaggedExperiment with 290322 rows and 345 columns
[8] SKCM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 473 columns
[9] SKCM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 355 columns
[10] SKCM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 452 columns
[11] SKCM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18071 rows and 473 columns
[12] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns
> rownames( SKCM )
CharacterList of length 12
[["SKCM_CNASeq-20160128"]] character(0)
[["SKCM_CNASNP-20160128"]] character(0)
[["SKCM_CNVSNP-20160128"]] character(0)
[["SKCM_GISTIC_AllByGene-20160128"]] character(0)
[["SKCM_GISTIC_Peaks-20160128"]] 21 22 1 2 3 23 24 4 ... 50 51 52 18 53 19 20
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["SKCM_Mutation-20160128"]] character(0)
[["SKCM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["SKCM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["SKCM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( SKCM )
CharacterList of length 12
[["SKCM_CNASeq-20160128"]] TCGA-BF-A1PU-01A-11D-A18Z-02 ...
[["SKCM_CNASNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_CNVSNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_AllByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_Peaks-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_Mutation-20160128"]] TCGA-BF-A1PU-01A-11D-A19A-08 ...
[["SKCM_RNASeq2Gene-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
[["SKCM_RPPAArray-20160128"]] TCGA-3N-A9WC-06A-21-A444-20 ...
[["SKCM_miRNASeqGene-20160128"]] TCGA-3N-A9WC-06A-11R-A38N-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 SKCM_CNASeq-20160128 0.9 Mb
2 SKCM_CNASNP-20160128 12.3 Mb
3 SKCM_CNVSNP-20160128 3.2 Mb
4 SKCM_GISTIC_AllByGene-20160128 73 Mb
5 SKCM_GISTIC_Peaks-20160128 0.3 Mb
6 SKCM_GISTIC_ThresholdedByGene-20160128 72.8 Mb
7 SKCM_Mutation-20160128 299.6 Mb
8 SKCM_RNASeq2Gene-20160128 76.6 Mb
9 SKCM_RPPAArray-20160128 0.7 Mb
10 SKCM_miRNASeqGene-20160128 3.8 Mb
11 SKCM_RNASeq2GeneNorm-20160128 67.5 Mb
12 SKCM_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
249 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 221 221 2.99 2.4 3.9
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.00 48.00 58.00 58.24 71.00 90.00 8
vital_status:
0 1
247 223
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
79 518 1093 1789 2073 10870 249
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2.0 477.5 1146.0 1885.3 2658.8 11252.0 230
days_to_submitted_specimen_dx:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2 0 344 1017 1372 10847 14
melanoma_ulceration:
no yes NA's
146 167 157
melanoma_primary_known:
no yes
47 423
Breslow_thickness:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.300 3.000 5.585 6.950 75.000 111
gender:
female male
180 290
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1978 2003 2008 2006 2011 2013 11
radiation_therapy:
no yes NA's
420 49 1
race:
asian black or african american white
12 1 447
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
11 446 13
Including an additional 1517 columns
A document describing the TCGA cancer code
Note. Only the colData has changed.
> experiments( SKCM )
ExperimentList class object of length 0:
> rownames( SKCM )
CharacterList of length 0
> colnames( SKCM )
CharacterList of length 0
Sizes of each ExperimentList element:
[1] assay size.Mb
<0 rows> (or 0-length row.names)
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
249 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 221 221 2.99 2.4 3.9
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.00 48.00 58.00 58.24 71.00 90.00 8
vital_status:
0 1
247 223
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
79 518 1093 1789 2073 10870 249
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2.0 477.5 1146.0 1885.3 2658.8 11252.0 230
days_to_submitted_specimen_dx:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-2 0 344 1017 1372 10847 14
melanoma_ulceration:
no yes NA's
146 167 157
melanoma_primary_known:
no yes
47 423
Breslow_thickness:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 1.300 3.000 5.585 6.950 75.000 111
gender:
female male
180 290
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1978 2003 2008 2006 2011 2013 11
radiation_therapy:
no yes NA's
420 49 1
race:
asian black or african american white
12 1 447
NA's
10
ethnicity:
hispanic or latino not hispanic or latino NA's
11 446 13
Including an additional 1517 columns
A document describing the TCGA cancer code
> experiments( STAD )
ExperimentList class object of length 14:
[1] STAD_CNASeq-20160128: RaggedExperiment with 31824 rows and 214 columns
[2] STAD_CNASNP-20160128: RaggedExperiment with 443042 rows and 906 columns
[3] STAD_CNVSNP-20160128: RaggedExperiment with 118389 rows and 904 columns
[4] STAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[5] STAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 84 rows and 441 columns
[6] STAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[7] STAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 430 columns
[8] STAD_Mutation-20160128: RaggedExperiment with 148520 rows and 289 columns
[9] STAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 450 columns
[10] STAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 450 columns
[11] STAD_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 271 columns
[12] STAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 357 columns
[13] STAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[14] STAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 397 columns
> rownames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] character(0)
[["STAD_CNASNP-20160128"]] character(0)
[["STAD_CNVSNP-20160128"]] character(0)
[["STAD_GISTIC_AllByGene-20160128"]] character(0)
[["STAD_GISTIC_Peaks-20160128"]] 1 37 38 2 3 39 40 ... 81 34 82 35 83 84 85
[["STAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["STAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["STAD_Mutation-20160128"]] character(0)
[["STAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["STAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] TCGA-B7-5816-01A-21D-1598-02 ...
[["STAD_CNASNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_CNVSNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_AllByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_Peaks-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_miRNASeqGene-20160128"]] TCGA-3M-AB46-01A-11R-A415-13 ...
[["STAD_Mutation-20160128"]] TCGA-B7-5816-01A-21D-1600-08 ...
[["STAD_RNASeq2Gene-20160128"]] TCGA-3M-AB46-01A-11R-A414-31 ...
[["STAD_RNASeq2GeneNorm-20160128"]] TCGA-3M-AB46-01A-11R-A414-31 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 STAD_CNASeq-20160128 0.9 Mb
2 STAD_CNASNP-20160128 12.1 Mb
3 STAD_CNVSNP-20160128 3.4 Mb
4 STAD_GISTIC_AllByGene-20160128 87 Mb
5 STAD_GISTIC_Peaks-20160128 0.4 Mb
6 STAD_GISTIC_ThresholdedByGene-20160128 86.8 Mb
7 STAD_miRNASeqGene-20160128 3.7 Mb
8 STAD_Mutation-20160128 161.5 Mb
9 STAD_RNASeq2Gene-20160128 73 Mb
10 STAD_RNASeq2GeneNorm-20160128 73 Mb
11 STAD_RNASeqGene-20160128 57.4 Mb
12 STAD_RPPAArray-20160128 0.6 Mb
13 STAD_Methylation_methyl27-20160128 4.9 Mb
14 STAD_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
273 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
170.000 170.000 0.948 0.792 1.085
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 58.00 67.00 65.73 73.00 90.00 9
vital_status:
0 1
268 175
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 194.0 346.0 423.7 553.5 2197.0 273
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 335.5 547.5 673.7 912.0 3720.0 177
tumor_tissue_site:
stomach
443
pathology_M_stage:
m0 m1 mx
391 30 22
gender:
female male
158 285
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2010 2011 2010 2012 2013 6
radiation_therapy:
no yes NA's
323 77 43
residual_tumor:
r0 r1 r2 rx NA's
350 18 19 25 31
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 3.000 5.635 8.000 57.000 51
race:
asian
89
black or african american
13
native hawaiian or other pacific islander
1
white
278
NA's
62
ethnicity:
hispanic or latino not hispanic or latino NA's
5 318 120
Including an additional 1390 columns
A document describing the TCGA cancer code
> experiments( STAD )
ExperimentList class object of length 14:
[1] STAD_CNASeq-20160128: RaggedExperiment with 31824 rows and 214 columns
[2] STAD_CNASNP-20160128: RaggedExperiment with 443042 rows and 906 columns
[3] STAD_CNVSNP-20160128: RaggedExperiment with 118389 rows and 904 columns
[4] STAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[5] STAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 84 rows and 441 columns
[6] STAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[7] STAD_Mutation-20160128: RaggedExperiment with 148520 rows and 289 columns
[8] STAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 450 columns
[9] STAD_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 271 columns
[10] STAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 357 columns
[11] STAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 430 columns
[12] STAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18664 rows and 450 columns
[13] STAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[14] STAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 397 columns
> rownames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] character(0)
[["STAD_CNASNP-20160128"]] character(0)
[["STAD_CNVSNP-20160128"]] character(0)
[["STAD_GISTIC_AllByGene-20160128"]] character(0)
[["STAD_GISTIC_Peaks-20160128"]] 1 37 38 2 3 39 40 ... 81 34 82 35 83 84 85
[["STAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["STAD_Mutation-20160128"]] character(0)
[["STAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["STAD_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
[["STAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<4 more elements>
> colnames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] TCGA-B7-5816-01A-21D-1598-02 ...
[["STAD_CNASNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_CNVSNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_AllByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_Peaks-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_Mutation-20160128"]] TCGA-B7-5816-01A-21D-1600-08 ...
[["STAD_RNASeq2Gene-20160128"]] TCGA-3M-AB46-01A-11R-A414-31 ...
[["STAD_RNASeqGene-20160128"]] TCGA-B7-5816-01A-21R-1602-13 ...
[["STAD_RPPAArray-20160128"]] TCGA-3M-AB47-01A-11-A43D-20 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 STAD_CNASeq-20160128 0.9 Mb
2 STAD_CNASNP-20160128 12.1 Mb
3 STAD_CNVSNP-20160128 3.4 Mb
4 STAD_GISTIC_AllByGene-20160128 87 Mb
5 STAD_GISTIC_Peaks-20160128 0.4 Mb
6 STAD_GISTIC_ThresholdedByGene-20160128 86.8 Mb
7 STAD_Mutation-20160128 161.5 Mb
8 STAD_RNASeq2Gene-20160128 73 Mb
9 STAD_RNASeqGene-20160128 57.4 Mb
10 STAD_RPPAArray-20160128 0.6 Mb
11 STAD_miRNASeqGene-20160128 3.7 Mb
12 STAD_RNASeq2GeneNorm-20160128 66.5 Mb
13 STAD_Methylation_methyl27-20160128 4.9 Mb
14 STAD_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
273 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 170 170 0.948 0.792 1.08
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 58.00 67.00 65.73 73.00 90.00 9
vital_status:
0 1
268 175
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 194.0 346.0 423.7 553.5 2197.0 273
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 335.5 547.5 673.7 912.0 3720.0 177
tumor_tissue_site:
stomach
443
pathology_M_stage:
m0 m1 mx
391 30 22
gender:
female male
158 285
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2010 2011 2010 2012 2013 6
radiation_therapy:
no yes NA's
323 77 43
residual_tumor:
r0 r1 r2 rx NA's
350 18 19 25 31
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 3.000 5.635 8.000 57.000 51
race:
asian
89
black or african american
13
native hawaiian or other pacific islander
1
white
278
NA's
62
ethnicity:
hispanic or latino not hispanic or latino NA's
5 318 120
Including an additional 1390 columns
A document describing the TCGA cancer code
> experiments( TGCT )
ExperimentList class object of length 11:
[1] TGCT_CNASNP-20160128: RaggedExperiment with 137968 rows and 271 columns
[2] TGCT_CNVSNP-20160128: RaggedExperiment with 25479 rows and 271 columns
[3] TGCT_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[4] TGCT_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 48 rows and 134 columns
[5] TGCT_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[6] TGCT_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 139 columns
[7] TGCT_Mutation-20160128: RaggedExperiment with 14672 rows and 138 columns
[8] TGCT_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 139 columns
[9] TGCT_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 139 columns
[10] TGCT_RPPAArray-20160128: SummarizedExperiment with 192 rows and 107 columns
[11] TGCT_Methylation-20160128: SummarizedExperiment with 485577 rows and 139 columns
> rownames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] character(0)
[["TGCT_CNVSNP-20160128"]] character(0)
[["TGCT_GISTIC_AllByGene-20160128"]] character(0)
[["TGCT_GISTIC_Peaks-20160128"]] 17 18 1 19 2 20 21 ... 44 45 47 46 48 15 16
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["TGCT_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["TGCT_Mutation-20160128"]] character(0)
[["TGCT_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["TGCT_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["TGCT_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_CNVSNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_AllByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_Peaks-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_miRNASeqGene-20160128"]] TCGA-2G-AAEW-01A-11R-A439-13 ...
[["TGCT_Mutation-20160128"]] TCGA-2G-AAEW-01A-11D-A42Y-10 ...
[["TGCT_RNASeq2Gene-20160128"]] TCGA-2G-AAEW-01A-11R-A430-07 ...
[["TGCT_RNASeq2GeneNorm-20160128"]] TCGA-2G-AAEW-01A-11R-A430-07 ...
[["TGCT_RPPAArray-20160128"]] TCGA-2G-AAEW-01A-21-A45P-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 TGCT_CNASNP-20160128 3.8 Mb
2 TGCT_CNVSNP-20160128 0.8 Mb
3 TGCT_GISTIC_AllByGene-20160128 28.8 Mb
4 TGCT_GISTIC_Peaks-20160128 0.1 Mb
5 TGCT_GISTIC_ThresholdedByGene-20160128 28.7 Mb
6 TGCT_miRNASeqGene-20160128 1.3 Mb
7 TGCT_Mutation-20160128 10 Mb
8 TGCT_RNASeq2Gene-20160128 24.3 Mb
9 TGCT_RNASeq2GeneNorm-20160128 24.3 Mb
10 TGCT_RPPAArray-20160128 0.2 Mb
11 TGCT_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
130 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
4.0000 4.0000 1.5493 0.0466 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 26.00 31.00 31.99 37.00 67.00
vital_status:
0 1
130 4
days_to_death:
17 513 618 6972 NA's
1 1 1 1 130
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 688.2 1265.5 2092.7 2826.2 7437.0 4
tumor_tissue_site:
testes
134
pathology_T_stage:
t1 t2 t3 tx
76 51 6 1
pathology_N_stage:
n0 n1 n2 nx NA's
46 11 2 65 10
pathology_M_stage:
m0 m1 m1a m1b NA's
115 2 1 1 15
gender:
male
134
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1992 2006 2009 2008 2012 2013
radiation_therapy:
no yes NA's
111 21 2
karnofsky_performance_score:
80 90 100 NA's
5 41 56 32
race:
asian black or african american white
4 6 119
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
12 111 11
Including an additional 762 columns
A document describing the TCGA cancer code
> experiments( TGCT )
ExperimentList class object of length 11:
[1] TGCT_CNASNP-20160128: RaggedExperiment with 137968 rows and 271 columns
[2] TGCT_CNVSNP-20160128: RaggedExperiment with 25479 rows and 271 columns
[3] TGCT_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[4] TGCT_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 48 rows and 134 columns
[5] TGCT_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
[6] TGCT_Mutation-20160128: RaggedExperiment with 14672 rows and 138 columns
[7] TGCT_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 139 columns
[8] TGCT_RPPAArray-20160128: SummarizedExperiment with 192 rows and 107 columns
[9] TGCT_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 139 columns
[10] TGCT_RNASeq2GeneNorm-20160128: SummarizedExperiment with 19036 rows and 139 columns
[11] TGCT_Methylation-20160128: SummarizedExperiment with 485577 rows and 139 columns
> rownames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] character(0)
[["TGCT_CNVSNP-20160128"]] character(0)
[["TGCT_GISTIC_AllByGene-20160128"]] character(0)
[["TGCT_GISTIC_Peaks-20160128"]] 17 18 1 19 2 20 21 ... 44 45 47 46 48 15 16
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["TGCT_Mutation-20160128"]] character(0)
[["TGCT_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["TGCT_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["TGCT_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["TGCT_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_CNVSNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_AllByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_Peaks-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_Mutation-20160128"]] TCGA-2G-AAEW-01A-11D-A42Y-10 ...
[["TGCT_RNASeq2Gene-20160128"]] TCGA-2G-AAEW-01A-11R-A430-07 ...
[["TGCT_RPPAArray-20160128"]] TCGA-2G-AAEW-01A-21-A45P-20 ...
[["TGCT_miRNASeqGene-20160128"]] TCGA-2G-AAEW-01A-11R-A439-13 ...
[["TGCT_RNASeq2GeneNorm-20160128"]] TCGA-2G-AAEW-01 ... TCGA-ZM-AA0N-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 TGCT_CNASNP-20160128 3.8 Mb
2 TGCT_CNVSNP-20160128 0.8 Mb
3 TGCT_GISTIC_AllByGene-20160128 28.8 Mb
4 TGCT_GISTIC_Peaks-20160128 0.1 Mb
5 TGCT_GISTIC_ThresholdedByGene-20160128 28.7 Mb
6 TGCT_Mutation-20160128 10 Mb
7 TGCT_RNASeq2Gene-20160128 24.3 Mb
8 TGCT_RPPAArray-20160128 0.2 Mb
9 TGCT_miRNASeqGene-20160128 1.3 Mb
10 TGCT_RNASeq2GeneNorm-20160128 22.6 Mb
11 TGCT_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
130 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 4 4 1.55 0.0466 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
14.00 26.00 31.00 31.99 37.00 67.00
vital_status:
0 1
130 4
days_to_death:
17 513 618 6972 NA's
1 1 1 1 130
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
3.0 688.2 1265.5 2092.7 2826.2 7437.0 4
tumor_tissue_site:
testes
134
pathology_T_stage:
t1 t2 t3 tx
76 51 6 1
pathology_N_stage:
n0 n1 n2 nx NA's
46 11 2 65 10
pathology_M_stage:
m0 m1 m1a m1b NA's
115 2 1 1 15
gender:
male
134
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1992 2006 2009 2008 2012 2013
radiation_therapy:
no yes NA's
111 21 2
karnofsky_performance_score:
80 90 100 NA's
5 41 56 32
race:
asian black or african american white
4 6 119
NA's
5
ethnicity:
hispanic or latino not hispanic or latino NA's
12 111 11
Including an additional 762 columns
A document describing the TCGA cancer code
> experiments( THCA )
ExperimentList class object of length 13:
[1] THCA_CNASeq-20160128: RaggedExperiment with 5953 rows and 203 columns
[2] THCA_CNASNP-20160128: RaggedExperiment with 389998 rows and 1013 columns
[3] THCA_CNVSNP-20160128: RaggedExperiment with 55117 rows and 1013 columns
[4] THCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[5] THCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 38 rows and 499 columns
[6] THCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[7] THCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 569 columns
[8] THCA_Mutation-20160128: RaggedExperiment with 7458 rows and 405 columns
[9] THCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 568 columns
[10] THCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 568 columns
[11] THCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 4 columns
[12] THCA_RPPAArray-20160128: SummarizedExperiment with 175 rows and 224 columns
[13] THCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 567 columns
> rownames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] character(0)
[["THCA_CNASNP-20160128"]] character(0)
[["THCA_CNVSNP-20160128"]] character(0)
[["THCA_GISTIC_AllByGene-20160128"]] character(0)
[["THCA_GISTIC_Peaks-20160128"]] 1 10 11 12 2 13 3 14 ... 36 37 38 39 7 40 41
[["THCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THCA_Mutation-20160128"]] character(0)
[["THCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<3 more elements>
> colnames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] TCGA-BJ-A0Z2-01A-11D-A10R-02 ...
[["THCA_CNASNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_CNVSNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_AllByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_Peaks-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_miRNASeqGene-20160128"]] TCGA-4C-A93U-01A-11R-A39B-13 ...
[["THCA_Mutation-20160128"]] TCGA-BJ-A0YZ-01A-11D-A10S-08 ...
[["THCA_RNASeq2Gene-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
[["THCA_RNASeq2GeneNorm-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 THCA_CNASeq-20160128 0.2 Mb
2 THCA_CNASNP-20160128 10.7 Mb
3 THCA_CNVSNP-20160128 1.8 Mb
4 THCA_GISTIC_AllByGene-20160128 97.8 Mb
5 THCA_GISTIC_Peaks-20160128 0.3 Mb
6 THCA_GISTIC_ThresholdedByGene-20160128 97.7 Mb
7 THCA_miRNASeqGene-20160128 4.8 Mb
8 THCA_Mutation-20160128 14 Mb
9 THCA_RNASeq2Gene-20160128 91.5 Mb
10 THCA_RNASeq2GeneNorm-20160128 91.5 Mb
11 THCA_RNASeqGene-20160128 3.2 Mb
12 THCA_RPPAArray-20160128 0.4 Mb
13 THCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
487 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
16.00 16.00 2.80 2.23 4.80
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
15.00 35.00 46.00 47.26 58.00 89.00
vital_status:
0 1
487 16
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
174 743 1021 1176 1631 2973 487
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 535 943 1220 1513 5423 16
tumor_tissue_site:
thyroid
503
pathology_N_stage:
n0 n1 n1a n1b nx
227 58 93 75 50
pathology_M_stage:
m0 m1 mx NA's
280 9 213 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1993 2008 2010 2009 2011 2013
radiation_therapy:
no yes NA's
181 306 16
radiation_exposure:
no yes NA's
423 17 63
extrathyroidal_extension:
minimal (t3) moderate/advanced (t4a) none
133 18 333
very advanced (t4b) NA's
1 18
residual_tumor:
r0 r1 r2 rx NA's
385 52 4 30 32
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 3.658 5.000 41.000 114
multifocality:
multifocal unifocal NA's
227 266 10
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.300 1.700 2.600 2.975 4.000 8.200 100
Including an additional 1481 columns
A document describing the TCGA cancer code
> experiments( THCA )
ExperimentList class object of length 13:
[1] THCA_CNASeq-20160128: RaggedExperiment with 5953 rows and 203 columns
[2] THCA_CNASNP-20160128: RaggedExperiment with 389998 rows and 1013 columns
[3] THCA_CNVSNP-20160128: RaggedExperiment with 55117 rows and 1013 columns
[4] THCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[5] THCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 38 rows and 499 columns
[6] THCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 499 columns
[7] THCA_Mutation-20160128: RaggedExperiment with 7458 rows and 405 columns
[8] THCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 568 columns
[9] THCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 4 columns
[10] THCA_RPPAArray-20160128: SummarizedExperiment with 175 rows and 224 columns
[11] THCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 569 columns
[12] THCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18003 rows and 568 columns
[13] THCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 567 columns
> rownames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] character(0)
[["THCA_CNASNP-20160128"]] character(0)
[["THCA_CNVSNP-20160128"]] character(0)
[["THCA_GISTIC_AllByGene-20160128"]] character(0)
[["THCA_GISTIC_Peaks-20160128"]] 1 10 11 12 2 13 3 14 ... 36 37 38 39 7 40 41
[["THCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THCA_Mutation-20160128"]] character(0)
[["THCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THCA_RPPAArray-20160128"]] 14-3-3_epsilon 4E-BP1 ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( THCA )
CharacterList of length 13
[["THCA_CNASeq-20160128"]] TCGA-BJ-A0Z2-01A-11D-A10R-02 ...
[["THCA_CNASNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_CNVSNP-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_AllByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_Peaks-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-4C-A93U-01A-11D-A396-01 ...
[["THCA_Mutation-20160128"]] TCGA-BJ-A0YZ-01A-11D-A10S-08 ...
[["THCA_RNASeq2Gene-20160128"]] TCGA-4C-A93U-01A-11R-A39I-07 ...
[["THCA_RNASeqGene-20160128"]] TCGA-DJ-A1QE-01A-21R-A14Y-07 ...
[["THCA_RPPAArray-20160128"]] TCGA-BJ-A0YZ-01A-21-A21L-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 THCA_CNASeq-20160128 0.2 Mb
2 THCA_CNASNP-20160128 10.7 Mb
3 THCA_CNVSNP-20160128 1.8 Mb
4 THCA_GISTIC_AllByGene-20160128 97.8 Mb
5 THCA_GISTIC_Peaks-20160128 0.3 Mb
6 THCA_GISTIC_ThresholdedByGene-20160128 97.7 Mb
7 THCA_Mutation-20160128 14 Mb
8 THCA_RNASeq2Gene-20160128 91.5 Mb
9 THCA_RNASeqGene-20160128 3.2 Mb
10 THCA_RPPAArray-20160128 0.4 Mb
11 THCA_miRNASeqGene-20160128 4.8 Mb
12 THCA_RNASeq2GeneNorm-20160128 80.3 Mb
13 THCA_Methylation-20160128 75.1 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
487 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 16 16 2.8 2.23 4.8
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
15.00 35.00 46.00 47.26 58.00 89.00
vital_status:
0 1
487 16
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
174 743 1021 1176 1631 2973 487
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0 535 943 1220 1513 5423 16
tumor_tissue_site:
thyroid
503
pathology_N_stage:
n0 n1 n1a n1b nx
227 58 93 75 50
pathology_M_stage:
m0 m1 mx NA's
280 9 213 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1993 2008 2010 2009 2011 2013
radiation_therapy:
no yes NA's
181 306 16
radiation_exposure:
no yes NA's
423 17 63
extrathyroidal_extension:
minimal (t3) moderate/advanced (t4a) none
133 18 333
very advanced (t4b) NA's
1 18
residual_tumor:
r0 r1 r2 rx NA's
385 52 4 30 32
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 3.658 5.000 41.000 114
multifocality:
multifocal unifocal NA's
227 266 10
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.300 1.700 2.600 2.975 4.000 8.200 100
Including an additional 1481 columns
A document describing the TCGA cancer code
> experiments( THYM )
ExperimentList class object of length 11:
[1] THYM_CNASNP-20160128: RaggedExperiment with 105646 rows and 248 columns
[2] THYM_CNVSNP-20160128: RaggedExperiment with 15571 rows and 248 columns
[3] THYM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[4] THYM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 123 columns
[5] THYM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[6] THYM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 126 columns
[7] THYM_Mutation-20160128: RaggedExperiment with 3064 rows and 123 columns
[8] THYM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 122 columns
[9] THYM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 122 columns
[10] THYM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 90 columns
[11] THYM_Methylation-20160128: SummarizedExperiment with 485577 rows and 126 columns
> rownames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] character(0)
[["THYM_CNVSNP-20160128"]] character(0)
[["THYM_GISTIC_AllByGene-20160128"]] character(0)
[["THYM_GISTIC_Peaks-20160128"]] 1 8 9 10 11 12 13 14 2 15 3 4 16 5 17 18
[["THYM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THYM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THYM_Mutation-20160128"]] character(0)
[["THYM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THYM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["THYM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>
> colnames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_CNVSNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_AllByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_Peaks-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_miRNASeqGene-20160128"]] TCGA-3G-AB0O-01A-22R-A42W-13 ...
[["THYM_Mutation-20160128"]] TCGA-3G-AB0O-01A-22D-A423-09 ...
[["THYM_RNASeq2Gene-20160128"]] TCGA-3G-AB0O-01A-22R-A42C-07 ...
[["THYM_RNASeq2GeneNorm-20160128"]] TCGA-3G-AB0O-01A-22R-A42C-07 ...
[["THYM_RPPAArray-20160128"]] TCGA-3G-AB0O-01A-11-A45R-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 THYM_CNASNP-20160128 2.9 Mb
2 THYM_CNVSNP-20160128 0.5 Mb
3 THYM_GISTIC_AllByGene-20160128 26.7 Mb
4 THYM_GISTIC_Peaks-20160128 0.1 Mb
5 THYM_GISTIC_ThresholdedByGene-20160128 26.6 Mb
6 THYM_miRNASeqGene-20160128 1.2 Mb
7 THYM_Mutation-20160128 3.3 Mb
8 THYM_RNASeq2Gene-20160128 21.7 Mb
9 THYM_RNASeq2GeneNorm-20160128 21.7 Mb
10 THYM_RPPAArray-20160128 0.2 Mb
11 THYM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
115 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
9.00 9.00 2.34 1.04 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.00 49.50 60.00 58.15 68.50 84.00 1
vital_status:
0 1
115 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
124 379 853 1423 2488 3488 115
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 725.2 1267.5 1486.3 1947.0 4575.0 10
tumor_tissue_site:
anterior mediastinum thymus
27 97
gender:
female male
60 64
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2008 2010 2010 2012 2013 1
radiation_therapy:
no yes
81 43
race:
asian black or african american white
13 6 103
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
10 100 14
Including an additional 685 columns
A document describing the TCGA cancer code
> experiments( THYM )
ExperimentList class object of length 11:
[1] THYM_CNASNP-20160128: RaggedExperiment with 105646 rows and 248 columns
[2] THYM_CNVSNP-20160128: RaggedExperiment with 15571 rows and 248 columns
[3] THYM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[4] THYM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 123 columns
[5] THYM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[6] THYM_Mutation-20160128: RaggedExperiment with 3064 rows and 123 columns
[7] THYM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 122 columns
[8] THYM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 90 columns
[9] THYM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 126 columns
[10] THYM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18286 rows and 122 columns
[11] THYM_Methylation-20160128: SummarizedExperiment with 485577 rows and 126 columns
> rownames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] character(0)
[["THYM_CNVSNP-20160128"]] character(0)
[["THYM_GISTIC_AllByGene-20160128"]] character(0)
[["THYM_GISTIC_Peaks-20160128"]] 1 8 9 10 11 12 13 14 2 15 3 4 16 5 17 18
[["THYM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THYM_Mutation-20160128"]] character(0)
[["THYM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THYM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["THYM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THYM_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_CNVSNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_AllByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_Peaks-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_Mutation-20160128"]] TCGA-3G-AB0O-01A-22D-A423-09 ...
[["THYM_RNASeq2Gene-20160128"]] TCGA-3G-AB0O-01A-22R-A42C-07 ...
[["THYM_RPPAArray-20160128"]] TCGA-3G-AB0O-01A-11-A45R-20 ...
[["THYM_miRNASeqGene-20160128"]] TCGA-3G-AB0O-01A-22R-A42W-13 ...
[["THYM_RNASeq2GeneNorm-20160128"]] TCGA-3G-AB0O-01 ... TCGA-ZT-A8OM-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 THYM_CNASNP-20160128 2.9 Mb
2 THYM_CNVSNP-20160128 0.5 Mb
3 THYM_GISTIC_AllByGene-20160128 26.7 Mb
4 THYM_GISTIC_Peaks-20160128 0.1 Mb
5 THYM_GISTIC_ThresholdedByGene-20160128 26.6 Mb
6 THYM_Mutation-20160128 3.3 Mb
7 THYM_RNASeq2Gene-20160128 21.7 Mb
8 THYM_RPPAArray-20160128 0.2 Mb
9 THYM_miRNASeqGene-20160128 1.2 Mb
10 THYM_RNASeq2GeneNorm-20160128 19.3 Mb
11 THYM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
115 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 9 9 2.34 1.04 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.00 49.50 60.00 58.15 68.50 84.00 1
vital_status:
0 1
115 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
124 379 853 1423 2488 3488 115
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 725.2 1267.5 1486.3 1947.0 4575.0 10
tumor_tissue_site:
anterior mediastinum thymus
27 97
gender:
female male
60 64
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2008 2010 2010 2012 2013 1
radiation_therapy:
no yes
81 43
race:
asian black or african american white
13 6 103
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
10 100 14
Including an additional 685 columns
A document describing the TCGA cancer code
> experiments( UCEC )
ExperimentList class object of length 16:
[1] UCEC_CNASeq-20160128: RaggedExperiment with 36400 rows and 213 columns
[2] UCEC_CNASNP-20160128: RaggedExperiment with 619412 rows and 1083 columns
[3] UCEC_CNVSNP-20160128: RaggedExperiment with 127094 rows and 1078 columns
[4] UCEC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[5] UCEC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 98 rows and 539 columns
[6] UCEC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[7] UCEC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 433 columns
[8] UCEC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 54 columns
[9] UCEC_Mutation-20160128: RaggedExperiment with 184861 rows and 248 columns
[10] UCEC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 190 columns
[11] UCEC_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 380 columns
[12] UCEC_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 190 columns
[13] UCEC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 269 columns
[14] UCEC_RPPAArray-20160128: SummarizedExperiment with 208 rows and 440 columns
[15] UCEC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 118 columns
[16] UCEC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 466 columns
> rownames( UCEC )
CharacterList of length 16
[["UCEC_CNASeq-20160128"]] character(0)
[["UCEC_CNASNP-20160128"]] character(0)
[["UCEC_CNVSNP-20160128"]] character(0)
[["UCEC_GISTIC_AllByGene-20160128"]] character(0)
[["UCEC_GISTIC_Peaks-20160128"]] 51 52 1 2 3 4 5 53 ... 98 45 46 47 99 48 100
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCEC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCEC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["UCEC_Mutation-20160128"]] character(0)
[["UCEC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<6 more elements>
> colnames( UCEC )
CharacterList of length 16
[["UCEC_CNASeq-20160128"]] TCGA-A5-A0G5-01A-11D-A043-02 ...
[["UCEC_CNASNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_CNVSNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_AllByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_Peaks-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_miRNASeqGene-20160128"]] TCGA-2E-A9G8-01A-11R-A404-13 ...
[["UCEC_mRNAArray-20160128"]] TCGA-A5-A0G2-01A-11R-A040-07 ...
[["UCEC_Mutation-20160128"]] TCGA-A5-A0G3-01A-11W-A062-09 ...
[["UCEC_RNASeq2Gene-20160128"]] TCGA-2E-A9G8-01A-11R-A40A-07 ...
...
<6 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UCEC_CNASeq-20160128 1 Mb
2 UCEC_CNASNP-20160128 16.9 Mb
3 UCEC_CNVSNP-20160128 3.7 Mb
4 UCEC_GISTIC_AllByGene-20160128 105.5 Mb
5 UCEC_GISTIC_Peaks-20160128 0.6 Mb
6 UCEC_GISTIC_ThresholdedByGene-20160128 105.3 Mb
7 UCEC_miRNASeqGene-20160128 3.7 Mb
8 UCEC_mRNAArray-20160128 9.6 Mb
9 UCEC_Mutation-20160128 73.1 Mb
10 UCEC_RNASeq2Gene-20160128 32.3 Mb
11 UCEC_RNASeq2GeneNorm_illuminaga-20160128 62 Mb
12 UCEC_RNASeq2GeneNorm_illuminahiseq-20160128 32.3 Mb
13 UCEC_RNASeqGene-20160128 44.7 Mb
14 UCEC_RPPAArray-20160128 0.8 Mb
15 UCEC_Methylation_methyl27-20160128 4.9 Mb
16 UCEC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Available sample meta-data:
---------------------------
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
50.0 367.0 709.0 881.8 1063.0 3423.0 457
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-6.0 543.0 948.5 1195.1 1753.2 6859.0 92
tumor_tissue_site:
endometrial other specify
547 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2007 2009 2009 2010 2013 9
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
145 404 729 1405 2096 4144 535
radiation_therapy:
no yes NA's
295 228 25
histological_type:
endometrioid endometrial adenocarcinoma
411
mixed serous and endometrioid
22
serous endometrial adenocarcinoma
115
residual_tumor:
r0 r1 r2 rx NA's
376 22 16 41 93
Including an additional 1779 columns
A document describing the TCGA cancer code
> experiments( UCEC )
ExperimentList class object of length 17:
[1] UCEC_CNASeq-20160128: RaggedExperiment with 36400 rows and 213 columns
[2] UCEC_CNASNP-20160128: RaggedExperiment with 619412 rows and 1083 columns
[3] UCEC_CNVSNP-20160128: RaggedExperiment with 127094 rows and 1078 columns
[4] UCEC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[5] UCEC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 98 rows and 539 columns
[6] UCEC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 539 columns
[7] UCEC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 54 columns
[8] UCEC_Mutation-20160128: RaggedExperiment with 184861 rows and 248 columns
[9] UCEC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 190 columns
[10] UCEC_RNASeq2GeneNorm_illuminaga-20160128: SummarizedExperiment with 20501 rows and 380 columns
[11] UCEC_RNASeq2GeneNorm_illuminahiseq-20160128: SummarizedExperiment with 20501 rows and 190 columns
[12] UCEC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 269 columns
[13] UCEC_RPPAArray-20160128: SummarizedExperiment with 208 rows and 440 columns
[14] UCEC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 433 columns
[15] UCEC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18515 rows and 569 columns
[16] UCEC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 118 columns
[17] UCEC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 466 columns
> rownames( UCEC )
CharacterList of length 17
[["UCEC_CNASeq-20160128"]] character(0)
[["UCEC_CNASNP-20160128"]] character(0)
[["UCEC_CNVSNP-20160128"]] character(0)
[["UCEC_GISTIC_AllByGene-20160128"]] character(0)
[["UCEC_GISTIC_Peaks-20160128"]] 51 52 1 2 3 4 5 53 ... 98 45 46 47 99 48 100
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCEC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["UCEC_Mutation-20160128"]] character(0)
[["UCEC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCEC_RNASeq2GeneNorm_illuminaga-20160128"]] A1BG A1CF ... psiTPTE22 tAKR
...
<7 more elements>
> colnames( UCEC )
CharacterList of length 17
[["UCEC_CNASeq-20160128"]] TCGA-A5-A0G5-01A-11D-A043-02 ...
[["UCEC_CNASNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_CNVSNP-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_AllByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_Peaks-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2E-A9G8-01A-11D-A402-01 ...
[["UCEC_mRNAArray-20160128"]] TCGA-A5-A0G2-01A-11R-A040-07 ...
[["UCEC_Mutation-20160128"]] TCGA-A5-A0G3-01A-11W-A062-09 ...
[["UCEC_RNASeq2Gene-20160128"]] TCGA-2E-A9G8-01A-11R-A40A-07 ...
[["UCEC_RNASeq2GeneNorm_illuminaga-20160128"]] TCGA-A5-A0G1-01A-11R-A118-07...
...
<7 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UCEC_CNASeq-20160128 1 Mb
2 UCEC_CNASNP-20160128 16.9 Mb
3 UCEC_CNVSNP-20160128 3.7 Mb
4 UCEC_GISTIC_AllByGene-20160128 105.5 Mb
5 UCEC_GISTIC_Peaks-20160128 0.6 Mb
6 UCEC_GISTIC_ThresholdedByGene-20160128 105.3 Mb
7 UCEC_mRNAArray-20160128 9.6 Mb
8 UCEC_Mutation-20160128 73.1 Mb
9 UCEC_RNASeq2Gene-20160128 32.3 Mb
10 UCEC_RNASeq2GeneNorm_illuminaga-20160128 62 Mb
11 UCEC_RNASeq2GeneNorm_illuminahiseq-20160128 32.3 Mb
12 UCEC_RNASeqGene-20160128 44.7 Mb
13 UCEC_RPPAArray-20160128 0.8 Mb
14 UCEC_miRNASeqGene-20160128 3.7 Mb
15 UCEC_RNASeq2GeneNorm-20160128 82.8 Mb
16 UCEC_Methylation_methyl27-20160128 4.9 Mb
17 UCEC_Methylation_methyl450-20160128 75.1 Mb
---------------------------
Available sample meta-data:
---------------------------
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
50.0 367.0 709.0 881.8 1063.0 3423.0 457
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-6.0 543.0 948.5 1195.1 1753.2 6859.0 92
tumor_tissue_site:
endometrial other specify
547 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1995 2007 2009 2009 2010 2013 9
days_to_last_known_alive:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
145 404 729 1405 2096 4144 535
radiation_therapy:
no yes NA's
295 228 25
histological_type:
endometrioid endometrial adenocarcinoma
411
mixed serous and endometrioid
22
serous endometrial adenocarcinoma
115
residual_tumor:
r0 r1 r2 rx NA's
376 22 16 41 93
Including an additional 1779 columns
A document describing the TCGA cancer code
> experiments( UCS )
ExperimentList class object of length 11:
[1] UCS_CNASNP-20160128: RaggedExperiment with 54944 rows and 111 columns
[2] UCS_CNVSNP-20160128: RaggedExperiment with 19298 rows and 111 columns
[3] UCS_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[4] UCS_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 56 rows and 56 columns
[5] UCS_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[6] UCS_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 56 columns
[7] UCS_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
[8] UCS_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 57 columns
[9] UCS_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 57 columns
[10] UCS_RPPAArray-20160128: SummarizedExperiment with 192 rows and 48 columns
[11] UCS_Methylation-20160128: SummarizedExperiment with 485577 rows and 57 columns
> rownames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] character(0)
[["UCS_CNVSNP-20160128"]] character(0)
[["UCS_GISTIC_AllByGene-20160128"]] character(0)
[["UCS_GISTIC_Peaks-20160128"]] 26 1 2 3 27 4 28 29 ... 21 22 56 57 23 24 58
[["UCS_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCS_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCS_Mutation-20160128"]] character(0)
[["UCS_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_CNVSNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_GISTIC_AllByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_Peaks-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_ThresholdedByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_miRNASeqGene-20160128"]] TCGA-N5-A4R8-01A-11R-A28Z-13 ...
[["UCS_Mutation-20160128"]] TCGA-N5-A4R8-01A-11D-A28R-08 ...
[["UCS_RNASeq2Gene-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RNASeq2GeneNorm-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RPPAArray-20160128"]] TCGA-N5-A4R8-01A-21-A41P-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 UCS_CNASNP-20160128 1.5 Mb
2 UCS_CNVSNP-20160128 0.6 Mb
3 UCS_GISTIC_AllByGene-20160128 14.1 Mb
4 UCS_GISTIC_Peaks-20160128 0.1 Mb
5 UCS_GISTIC_ThresholdedByGene-20160128 13.9 Mb
6 UCS_miRNASeqGene-20160128 0.6 Mb
7 UCS_Mutation-20160128 19.7 Mb
8 UCS_RNASeq2Gene-20160128 11.5 Mb
9 UCS_RNASeq2GeneNorm-20160128 11.5 Mb
10 UCS_RPPAArray-20160128 0.1 Mb
11 UCS_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
22 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
35.00 35.00 1.43 1.04 1.96
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
51.00 62.00 68.00 69.72 76.00 90.00
vital_status:
0 1
22 35
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 304.0 522.0 705.4 790.5 3115.0 22
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 591.2 828.0 1183.4 1647.5 4269.0 35
tumor_tissue_site:
uterus
57
gender:
female
57
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2002 2007 2009 2009 2011 2012
radiation_therapy:
no yes NA's
29 25 3
histological_type:
uterine carcinosarcoma/ malignant mixed mullerian tumor (mmmt): nos
24
uterine carcinosarcoma/ mmmt: heterologous type
20
uterine carcinosarcoma/mmmt: homologous type
13
race:
asian black or african american white
3 9 44
NA's
1
ethnicity:
hispanic or latino not hispanic or latino NA's
1 43 13
Including an additional 632 columns
A document describing the TCGA cancer code
> experiments( UCS )
ExperimentList class object of length 11:
[1] UCS_CNASNP-20160128: RaggedExperiment with 54944 rows and 111 columns
[2] UCS_CNVSNP-20160128: RaggedExperiment with 19298 rows and 111 columns
[3] UCS_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[4] UCS_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 56 rows and 56 columns
[5] UCS_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[6] UCS_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
[7] UCS_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 57 columns
[8] UCS_RPPAArray-20160128: SummarizedExperiment with 192 rows and 48 columns
[9] UCS_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 56 columns
[10] UCS_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18645 rows and 57 columns
[11] UCS_Methylation-20160128: SummarizedExperiment with 485577 rows and 57 columns
> rownames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] character(0)
[["UCS_CNVSNP-20160128"]] character(0)
[["UCS_GISTIC_AllByGene-20160128"]] character(0)
[["UCS_GISTIC_Peaks-20160128"]] 26 1 2 3 27 4 28 29 ... 21 22 56 57 23 24 58
[["UCS_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCS_Mutation-20160128"]] character(0)
[["UCS_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["UCS_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCS_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_CNVSNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_GISTIC_AllByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_Peaks-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_ThresholdedByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_Mutation-20160128"]] TCGA-N5-A4R8-01A-11D-A28R-08 ...
[["UCS_RNASeq2Gene-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RPPAArray-20160128"]] TCGA-N5-A4R8-01A-21-A41P-20 ...
[["UCS_miRNASeqGene-20160128"]] TCGA-N5-A4R8-01A-11R-A28Z-13 ...
[["UCS_RNASeq2GeneNorm-20160128"]] TCGA-N5-A4R8-01 ... TCGA-QN-A5NN-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 UCS_CNASNP-20160128 1.5 Mb
2 UCS_CNVSNP-20160128 0.6 Mb
3 UCS_GISTIC_AllByGene-20160128 14.1 Mb
4 UCS_GISTIC_Peaks-20160128 0.1 Mb
5 UCS_GISTIC_ThresholdedByGene-20160128 13.9 Mb
6 UCS_Mutation-20160128 19.7 Mb
7 UCS_RNASeq2Gene-20160128 11.5 Mb
8 UCS_RPPAArray-20160128 0.1 Mb
9 UCS_miRNASeqGene-20160128 0.6 Mb
10 UCS_RNASeq2GeneNorm-20160128 10.4 Mb
11 UCS_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
22 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 35 35 1.43 1.04 1.96
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
51.00 62.00 68.00 69.72 76.00 90.00
vital_status:
0 1
22 35
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 304.0 522.0 705.4 790.5 3115.0 22
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 591.2 828.0 1183.4 1647.5 4269.0 35
tumor_tissue_site:
uterus
57
gender:
female
57
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2002 2007 2009 2009 2011 2012
radiation_therapy:
no yes NA's
29 25 3
histological_type:
uterine carcinosarcoma/ malignant mixed mullerian tumor (mmmt): nos
24
uterine carcinosarcoma/ mmmt: heterologous type
20
uterine carcinosarcoma/mmmt: homologous type
13
race:
asian black or african american white
3 9 44
NA's
1
ethnicity:
hispanic or latino not hispanic or latino NA's
1 43 13
Including an additional 632 columns
A document describing the TCGA cancer code
> experiments( UVM )
ExperimentList class object of length 12:
[1] UVM_CNASeq-20160128: RaggedExperiment with 6496 rows and 102 columns
[2] UVM_CNASNP-20160128: RaggedExperiment with 69487 rows and 160 columns
[3] UVM_CNVSNP-20160128: RaggedExperiment with 12973 rows and 160 columns
[4] UVM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[5] UVM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 80 columns
[6] UVM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[7] UVM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[8] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
[9] UVM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 80 columns
[10] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 80 columns
[11] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns
[12] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] character(0)
[["UVM_CNASNP-20160128"]] character(0)
[["UVM_CNVSNP-20160128"]] character(0)
[["UVM_GISTIC_AllByGene-20160128"]] character(0)
[["UVM_GISTIC_Peaks-20160128"]] 4 5 6 7 8 9 10 11 ... 2 16 17 18 19 20 21 3
[["UVM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UVM_Mutation-20160128"]] character(0)
[["UVM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UVM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>
> colnames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] TCGA-RZ-AB0B-01A-11D-A40D-26 ...
[["UVM_CNASNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_CNVSNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_AllByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_Peaks-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ...
[["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ...
[["UVM_RNASeq2Gene-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
[["UVM_RNASeq2GeneNorm-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UVM_CNASeq-20160128 0.2 Mb
2 UVM_CNASNP-20160128 1.9 Mb
3 UVM_CNVSNP-20160128 0.4 Mb
4 UVM_GISTIC_AllByGene-20160128 18.5 Mb
5 UVM_GISTIC_Peaks-20160128 0.1 Mb
6 UVM_GISTIC_ThresholdedByGene-20160128 18.5 Mb
7 UVM_miRNASeqGene-20160128 0.8 Mb
8 UVM_Mutation-20160128 12.3 Mb
9 UVM_RNASeq2Gene-20160128 15.1 Mb
10 UVM_RNASeq2GeneNorm-20160128 15.1 Mb
11 UVM_RPPAArray-20160128 0.1 Mb
12 UVM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
23.00 23.00 1.66 1.14 3.05
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
22.00 51.00 61.50 61.65 74.25 86.00
vital_status:
0 1
57 23
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.0 393.5 606.0 693.9 1029.0 1581.0 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 495.0 821.0 861.9 1184.0 2600.0 23
tumor_tissue_site:
choroid
80
pathology_N_stage:
n0 nx NA's
52 27 1
pathology_M_stage:
m0 m1 m1b mx NA's
51 2 2 23 2
gender:
female male
35 45
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2007 2011 2012 2012 2013 2013
radiation_therapy:
no yes NA's
76 3 1
race:
white NA's
55 25
ethnicity:
hispanic or latino not hispanic or latino NA's
1 52 27
Including an additional 448 columns
A document describing the TCGA cancer code
> experiments( UVM )
ExperimentList class object of length 12:
[1] UVM_CNASeq-20160128: RaggedExperiment with 6496 rows and 102 columns
[2] UVM_CNASNP-20160128: RaggedExperiment with 69487 rows and 160 columns
[3] UVM_CNVSNP-20160128: RaggedExperiment with 12973 rows and 160 columns
[4] UVM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[5] UVM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 80 columns
[6] UVM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
[7] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
[8] UVM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 80 columns
[9] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns
[10] UVM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[11] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17345 rows and 80 columns
[12] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] character(0)
[["UVM_CNASNP-20160128"]] character(0)
[["UVM_CNVSNP-20160128"]] character(0)
[["UVM_GISTIC_AllByGene-20160128"]] character(0)
[["UVM_GISTIC_Peaks-20160128"]] 4 5 6 7 8 9 10 11 ... 2 16 17 18 19 20 21 3
[["UVM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UVM_Mutation-20160128"]] character(0)
[["UVM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UVM_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] TCGA-RZ-AB0B-01A-11D-A40D-26 ...
[["UVM_CNASNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_CNVSNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_AllByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_Peaks-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ...
[["UVM_RNASeq2Gene-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
[["UVM_RPPAArray-20160128"]] TCGA-V3-A9ZX-01A-21-A41Z-20 ...
[["UVM_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 UVM_CNASeq-20160128 0.2 Mb
2 UVM_CNASNP-20160128 1.9 Mb
3 UVM_CNVSNP-20160128 0.4 Mb
4 UVM_GISTIC_AllByGene-20160128 18.5 Mb
5 UVM_GISTIC_Peaks-20160128 0.1 Mb
6 UVM_GISTIC_ThresholdedByGene-20160128 18.5 Mb
7 UVM_Mutation-20160128 12.3 Mb
8 UVM_RNASeq2Gene-20160128 15.1 Mb
9 UVM_RPPAArray-20160128 0.1 Mb
10 UVM_miRNASeqGene-20160128 0.8 Mb
11 UVM_RNASeq2GeneNorm-20160128 12.8 Mb
12 UVM_Methylation-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
57 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 23 23 1.66 1.14 3.05
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
22.00 51.00 61.50 61.65 74.25 86.00
vital_status:
0 1
57 23
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.0 393.5 606.0 693.9 1029.0 1581.0 57
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 495.0 821.0 861.9 1184.0 2600.0 23
tumor_tissue_site:
choroid
80
pathology_N_stage:
n0 nx NA's
52 27 1
pathology_M_stage:
m0 m1 m1b mx NA's
51 2 2 23 2
gender:
female male
35 45
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2007 2011 2012 2012 2013 2013
radiation_therapy:
no yes NA's
76 3 1
race:
white NA's
55 25
ethnicity:
hispanic or latino not hispanic or latino NA's
1 52 27
Including an additional 448 columns