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Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: Release (3.19)

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.

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

Maintainer: Marcel Ramos <marcel.ramos at>

Citation (from within R, enter citation("RaggedExperiment")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

ASCAT to RaggedExperiment HTML R Script
RaggedExperiment HTML R Script
Reference Manual PDF


biocViews DataRepresentation, Infrastructure, Software
Version 1.28.1
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 4.2.0), GenomicRanges(>= 1.37.17)
Imports BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
Linking To
Depends On Me CNVRanger, SARC, curatedPCaData
Imports Me cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata, MOCHA
Suggests Me maftools, MultiAssayExperiment, MultiDataSet, TENxIO, curatedTCGAData, SingleCellMultiModal
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package RaggedExperiment_1.28.1.tar.gz
Windows Binary
macOS Binary (x86_64) RaggedExperiment_1.28.1.tgz
macOS Binary (arm64) RaggedExperiment_1.28.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive