Package: RaggedExperiment 1.37.0

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]

RaggedExperiment_1.37.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
RaggedExperiment/json (API)
NEWS

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

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

Pkgdown/docs site:https://bioconductor.github.io

On BioConductor:RaggedExperiment-1.37.0(bioc 3.24)RaggedExperiment-1.36.0(bioc 3.23)

infrastructuredatarepresentationcopynumbercore-packagedata-structuremutationsu24ca289073

8.71 score 5 stars 14 packages 102 scripts 29 exports 18 dependencies

Last updated from:78b3addd7c. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE247
source / vignettesOK249
linux-release-x86_64NOTE244
macos-release-arm64NOTE189
macos-oldrel-arm64NOTE170
windows-develNOTE165
windows-releaseNOTE203
windows-oldrelNOTE210
wasm-releaseOK113

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

Dependencies:abindBiobaseBiocBaseUtilsBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

ASCAT to RaggedExperiment

Lydia King, Marcel Ramos

Rendered fromASCAT_to_RaggedExperiment.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-07-10
Started: 2023-05-03

RaggedExperiment

Martin Morgan, Marcel Ramos

Rendered fromRaggedExperiment.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-07-10
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