This document serves as a reporting tool for errors that occur when running our utility functions on the cBioPortal datasets.
cBioPortalData()
)Typically, the number of errors encountered via the API are low. There are only a handful of packages that error when we apply the utility functions to provide a MultiAssayExperiment data representation.
First, we load the error Rda
dataset.
api_errs <- system.file(
"extdata", "api", "err_api_info.rda",
package = "cBioPortalData", mustWork = TRUE
)
load(api_errs)
We can now inspect the contents of the data:
## [1] "list"
## [1] 6
## Barcodes must start with 'TCGA'
## 2
## group length is 0 but data length > 0
## 1
## Frequency of NA values higher than the cutoff tolerance
## 2
## Inconsistent build numbers found
## 33
## `n` must be a single number, not an integer `NA`.
## 1
## Argument 1 must be a data frame or a named atomic vector.
## 1
There were about 6 unique errors during the last build run.
## [1] "Barcodes must start with 'TCGA'"
## [2] "group length is 0 but data length > 0"
## [3] "Frequency of NA values higher than the cutoff tolerance"
## [4] "Inconsistent build numbers found"
## [5] "`n` must be a single number, not an integer `NA`."
## [6] "Argument 1 must be a data frame or a named atomic vector."
The most common error was
Inconsistent build numbers found
. This is due to
annotations from different build numbers that were not able to be
resolved.
To see what datasets (cancer_study_id
s) have that error
we can use:
## [1] "msk_ch_2020" "msk_access_2021"
## [3] "mixed_msk_tcga_2021" "mixed_impact_subset_2022"
## [5] "pan_origimed_2020" "prad_msk_stopsack_2021"
## [7] "pancan_pcawg_2020" "prad_pik3r1_msk_2021"
## [9] "skcm_tcga" "stad_tcga"
## [11] "stad_tcga_pub" "skcm_tcga_pan_can_atlas_2018"
## [13] "stad_tcga_pan_can_atlas_2018" "stes_tcga_pub"
## [15] "summit_2018" "cfdna_msk_2019"
## [17] "blca_bcan_hcrn_2022" "nsclc_ctdx_msk_2022"
## [19] "thyroid_mskcc_2016" "skcm_mskcc_2014"
## [21] "tmb_mskcc_2018" "rectal_msk_2019"
## [23] "skcm_tcga_pub_2015" "msk_spectrum_tme_2022"
## [25] "ucec_ccr_cfdna_msk_2022" "paired_bladder_2022"
## [27] "mtnn_msk_2022" "pog570_bcgsc_2020"
## [29] "sarcoma_msk_2023" "bowel_colitis_msk_2022"
## [31] "luad_mskcc_2023_met_organotropism" "coad_silu_2022"
## [33] "paac_msk_jco_2023"
We can also have a look at the entirety of the dataset.
## $`Barcodes must start with 'TCGA'`
## [1] "blca_msk_tcga_2020" "nsclc_tcga_broad_2016"
##
## $`group length is 0 but data length > 0`
## [1] "glioma_msk_2018"
##
## $`Frequency of NA values higher than the cutoff tolerance`
## [1] "mixed_selpercatinib_2020" "ucec_ccr_msk_2022"
##
## $`Inconsistent build numbers found`
## [1] "msk_ch_2020" "msk_access_2021"
## [3] "mixed_msk_tcga_2021" "mixed_impact_subset_2022"
## [5] "pan_origimed_2020" "prad_msk_stopsack_2021"
## [7] "pancan_pcawg_2020" "prad_pik3r1_msk_2021"
## [9] "skcm_tcga" "stad_tcga"
## [11] "stad_tcga_pub" "skcm_tcga_pan_can_atlas_2018"
## [13] "stad_tcga_pan_can_atlas_2018" "stes_tcga_pub"
## [15] "summit_2018" "cfdna_msk_2019"
## [17] "blca_bcan_hcrn_2022" "nsclc_ctdx_msk_2022"
## [19] "thyroid_mskcc_2016" "skcm_mskcc_2014"
## [21] "tmb_mskcc_2018" "rectal_msk_2019"
## [23] "skcm_tcga_pub_2015" "msk_spectrum_tme_2022"
## [25] "ucec_ccr_cfdna_msk_2022" "paired_bladder_2022"
## [27] "mtnn_msk_2022" "pog570_bcgsc_2020"
## [29] "sarcoma_msk_2023" "bowel_colitis_msk_2022"
## [31] "luad_mskcc_2023_met_organotropism" "coad_silu_2022"
## [33] "paac_msk_jco_2023"
##
## $``n` must be a single number, not an integer `NA`.`
## [1] "msk_met_2021"
##
## $`Argument 1 must be a data frame or a named atomic vector.`
## [1] "makeanimpact_ccr_2023"
cBioDataPack()
Now let’s look at the errors in the packaged datasets that are used
for cBioDataPack
:
pack_errs <- system.file(
"extdata", "pack", "err_pack_info.rda",
package = "cBioPortalData", mustWork = TRUE
)
load(pack_errs)
We can do the same for this data:
## [1] 5
## more columns than column names
## 9
## Frequency of NA values higher than the cutoff tolerance
## 5
## non-character argument
## 2
## invalid class "ExperimentList" object: \n Non-unique names provided
## 2
## 'wget' call had nonzero exit status
## 11
We can get a list of all the errors present:
## [1] "more columns than column names"
## [2] "Frequency of NA values higher than the cutoff tolerance"
## [3] "non-character argument"
## [4] "invalid class \"ExperimentList\" object: \n Non-unique names provided"
## [5] "'wget' call had nonzero exit status"
And finally the full list of errors:
## $`more columns than column names`
## [1] "ccrcc_utokyo_2013" "coadread_tcga_pan_can_atlas_2018"
## [3] "gbm_cptac_2021" "ov_tcga_pan_can_atlas_2018"
## [5] "pan_origimed_2020" "sarc_tcga_pan_can_atlas_2018"
## [7] "luad_mskimpact_2021" "mbl_dkfz_2017"
## [9] "brca_tcga_pan_can_atlas_2018"
##
## $`Frequency of NA values higher than the cutoff tolerance`
## [1] "ihch_mskcc_2020" "ihch_msk_2021"
## [3] "mixed_selpercatinib_2020" "mixed_msk_tcga_2021"
## [5] "ucec_ccr_msk_2022"
##
## $`non-character argument`
## [1] "mbn_mdacc_2013" "pcpg_tcga_pub"
##
## $`invalid class "ExperimentList" object: \n Non-unique names provided`
## [1] "stad_tcga_pub" "mpnst_mskcc"
##
## $`'wget' call had nonzero exit status`
## [1] "makeanimpact_ccr_2023" "prad_organoids_msk_2022"
## [3] "mtnn_msk_2022" "sarcoma_msk_2023"
## [5] "bowel_colitis_msk_2022" "bladder_mskcc_2022"
## [7] "paac_msk_jco_2023" "nbl_msk_2023"
## [9] "rms_msk_2023" "gist_msk_2023"
## [11] "egc_trap_ccr_msk_2023"
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] survminer_0.4.9 ggpubr_0.6.0
## [3] ggplot2_3.5.1 survival_3.7-0
## [5] cBioPortalData_2.17.1 MultiAssayExperiment_1.31.4
## [7] SummarizedExperiment_1.35.1 Biobase_2.65.0
## [9] GenomicRanges_1.57.1 GenomeInfoDb_1.41.1
## [11] IRanges_2.39.2 S4Vectors_0.43.2
## [13] BiocGenerics_0.51.0 MatrixGenerics_1.17.0
## [15] matrixStats_1.3.0 AnVIL_1.17.11
## [17] AnVILBase_0.99.25 dplyr_1.1.4
## [19] BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] sys_3.4.2 jsonlite_1.8.8
## [3] magrittr_2.0.3 GenomicFeatures_1.57.0
## [5] farver_2.1.2 rmarkdown_2.28
## [7] BiocIO_1.15.1 zlibbioc_1.51.1
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.21.1 RCurl_1.98-1.16
## [13] rstatix_0.7.2 htmltools_0.5.8.1
## [15] S4Arrays_1.5.7 BiocBaseUtils_1.7.0
## [17] lambda.r_1.2.4 curl_5.2.1
## [19] broom_1.0.6 SparseArray_1.5.31
## [21] sass_0.4.9 bslib_0.8.0
## [23] htmlwidgets_1.6.4 httr2_1.0.3
## [25] zoo_1.8-12 futile.options_1.0.1
## [27] cachem_1.1.0 commonmark_1.9.1
## [29] buildtools_1.0.0 GenomicAlignments_1.41.0
## [31] mime_0.12 lifecycle_1.0.4
## [33] pkgconfig_2.0.3 Matrix_1.7-0
## [35] R6_2.5.1 fastmap_1.2.0
## [37] GenomeInfoDbData_1.2.12 shiny_1.9.1
## [39] digest_0.6.37 colorspace_2.1-1
## [41] RaggedExperiment_1.29.1 AnnotationDbi_1.67.0
## [43] RSQLite_2.3.7 labeling_0.4.3
## [45] filelock_1.0.3 RTCGAToolbox_2.35.0
## [47] km.ci_0.5-6 fansi_1.0.6
## [49] RJSONIO_1.3-1.9 httr_1.4.7
## [51] abind_1.4-5 compiler_4.4.1
## [53] bit64_4.0.5 withr_3.0.1
## [55] backports_1.5.0 BiocParallel_1.39.0
## [57] carData_3.0-5 DBI_1.2.3
## [59] highr_0.11 ggsignif_0.6.4
## [61] rappdirs_0.3.3 DelayedArray_0.31.11
## [63] rjson_0.2.22 tools_4.4.1
## [65] httpuv_1.6.15 glue_1.7.0
## [67] restfulr_0.0.15 promises_1.3.0
## [69] gridtext_0.1.5 grid_4.4.1
## [71] generics_0.1.3 gtable_0.3.5
## [73] KMsurv_0.1-5 tzdb_0.4.0
## [75] tidyr_1.3.1 data.table_1.15.4
## [77] hms_1.1.3 car_3.1-2
## [79] xml2_1.3.6 utf8_1.2.4
## [81] XVector_0.45.0 markdown_1.13
## [83] pillar_1.9.0 stringr_1.5.1
## [85] later_1.3.2 splines_4.4.1
## [87] ggtext_0.1.2 BiocFileCache_2.13.0
## [89] lattice_0.22-6 rtracklayer_1.65.0
## [91] bit_4.0.5 tidyselect_1.2.1
## [93] maketools_1.3.0 Biostrings_2.73.1
## [95] miniUI_0.1.1.1 knitr_1.48
## [97] gridExtra_2.3 futile.logger_1.4.3
## [99] xfun_0.47 DT_0.33
## [101] stringi_1.8.4 UCSC.utils_1.1.0
## [103] yaml_2.3.10 evaluate_0.24.0
## [105] codetools_0.2-20 tibble_3.2.1
## [107] BiocManager_1.30.24 cli_3.6.3
## [109] xtable_1.8-4 munsell_0.5.1
## [111] jquerylib_0.1.4 survMisc_0.5.6
## [113] Rcpp_1.0.13 GenomicDataCommons_1.29.3
## [115] dbplyr_2.5.0 png_0.1-8
## [117] XML_3.99-0.17 rapiclient_0.1.6
## [119] parallel_4.4.1 TCGAutils_1.25.0
## [121] readr_2.1.5 blob_1.2.4
## [123] bitops_1.0-8 scales_1.3.0
## [125] purrr_1.0.2 crayon_1.5.3
## [127] rlang_1.1.4 KEGGREST_1.45.1
## [129] rvest_1.0.4 formatR_1.14