Package: RaggedExperiment 1.31.1

RaggedExperiment: Representation of Sparse Experiments and Assays Across Samples

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

Authors:Martin Morgan [aut], Marcel Ramos [aut, cre], Lydia King [ctb]

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RaggedExperiment.pdf |RaggedExperiment.html✨
RaggedExperiment/json (API)
NEWS

# Install 'RaggedExperiment' in R:
install.packages('RaggedExperiment', repos = c('https://link-ny.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/raggedexperiment/issues

On BioConductor:RaggedExperiment-1.31.0(bioc 3.21)RaggedExperiment-1.30.0(bioc 3.20)

infrastructuredatarepresentationcopynumbercore-packagedata-structuremutations

8.79 score 4 stars 13 packages 74 scripts 29 exports 30 dependencies

Last updated 1 days agofrom:3c81b9a801. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macNOTENov 22 2024

Exports:as.data.frameas.listassayassayNamesassayscoercecolDatacolData<-compactAssaycompactSummarizedExperimentdisjoinAssaydisjoinSummarizedExperimentmcolsmcols<-overlapsAnyqreduceAssayqreduceSummarizedExperimentRaggedExperimentrowDatarowData<-rowRangesrowRanges<-seqinfoseqinfo<-showsparseAssaysparseSummarizedExperimentsubsetsubsetByOverlaps

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

ASCAT to RaggedExperiment

Lydia King, Marcel Ramos

Rendered fromASCAT_to_RaggedExperiment.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-17
Started: 2023-05-03

RaggedExperiment

Martin Morgan, Marcel Ramos

Rendered fromRaggedExperiment.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-17
Started: 2017-03-28

Readme and manuals

Help Manual

Help pageTopics
RaggedExperiment: Range-based data representation packageRaggedExperiment-package
Create simplified representation of ragged assay data.assay-functions compactAssay disjoinAssay qreduceAssay sparseAssay
RaggedExperiment objects$,RaggedExperiment-method as.data.frame,RaggedExperiment-method as.list,RaggedExperiment-method assay,RaggedExperiment,ANY-method assay,RaggedExperiment,missing-method assayNames,RaggedExperiment-method assays,RaggedExperiment-method class:RaggedExperiment coerce,GRangesList,RaggedExperiment-method coerce,RaggedExperiment,GRangesList-method colData,RaggedExperiment-method colData<-,RaggedExperiment,DataFrame-method dim,RaggedExperiment-method dimnames,RaggedExperiment-method dimnames<-,RaggedExperiment,ANY-method dimnames<-,RaggedExperiment,list-method length,RaggedExperiment-method mcols,RaggedExperiment-method mcols<-,RaggedExperiment-method overlapsAny,RaggedExperiment,Vector-method RaggedExperiment RaggedExperiment-class rowData,RaggedExperiment-method rowData<-,RaggedExperiment-method rowRanges,RaggedExperiment-method rowRanges<-,RaggedExperiment,GRanges-method seqinfo,RaggedExperiment-method seqinfo<-,RaggedExperiment-method show,RaggedExperiment-method subset,RaggedExperiment-method subsetByOverlaps,RaggedExperiment,Vector-method [,RaggedExperiment,ANY,ANY,ANY-method
Create SummarizedExperiment representations by transforming ragged assays to rectangular form.coerce,dgCMatrix,RaggedExperiment-method coerce-RaggedExperiment compactSummarizedExperiment disjoinSummarizedExperiment qreduceSummarizedExperiment sparseSummarizedExperiment