Package: RaggedExperiment 1.37.0

Marcel Ramos

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✨
DESCRIPTION |NEWS
card.svg |card.png
RaggedExperiment/json (API)

# Install 'RaggedExperiment' in R:
install.packages('RaggedExperiment', repos = c('https://bioc.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

8.61 score 5 stars 14 packages 107 scripts 1 mentions 29 exports 18 dependencies

Last updated from:78b3addd7c. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE153
linux-devel-x86_64NOTE302
source / vignettesOK262
linux-release-x86_64NOTE297
macos-release-arm64NOTE155
macos-oldrel-arm64NOTE146
windows-develNOTE189
windows-releaseNOTE184
windows-oldrelNOTE192
wasm-releaseOK127

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

Dependencies:abindBiobaseBiocBaseUtilsBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector

RaggedExperiment
Introduction | Installation | Citing RaggedExperiment | RaggedExperiment class overview | Constructing a RaggedExperiment object | Using GRanges objects | Using a GRangesList instance | Using a list of GRanges | Using a List of GRanges with metadata | Accessors | Range data | Dimension names | colData | Subsetting | by dimension | by genomic ranges | *Assay functions | sparseAssay | Support for sparse matrix output | compactAssay | disjoinAssay | qreduceAssay | Coercion | from dgCMatrix to RaggedExperiment | Session Information | References
Rendered fromRaggedExperiment.Rmdusingknitr::rmarkdown

Last update: 2025-07-10
Started: 2017-03-28

ASCAT to RaggedExperiment
Introduction | Installation | Structure of ASCAT data | Converting ASCAT data to GRanges format | ASCAT to GRanges objects | ASCAT to GRangesList instance | Constructing a RaggedExperiment object from ASCAT output | Using GRanges objects | Using a GRangesList instance | Downstream Analysis | Session Information
Rendered fromASCAT_to_RaggedExperiment.Rmdusingknitr::rmarkdown

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

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