RaggedExperiment

Representation of Sparse Experiments and Assays Across Samples


Bioconductor version: Release (3.20)

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 sph.cuny.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RaggedExperiment")

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

Documentation

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

browseVignettes("RaggedExperiment")
ASCAT to RaggedExperiment HTML R Script
RaggedExperiment HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.30.0
In Bioconductor since BioC 3.5 (R-3.4) (7.5 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
URL
Bug Reports https://github.com/Bioconductor/RaggedExperiment/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
Linking To
Enhances
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
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RaggedExperiment_1.30.0.tar.gz
Windows Binary (x86_64) RaggedExperiment_1.30.0.zip
macOS Binary (x86_64) RaggedExperiment_1.30.0.tgz
macOS Binary (arm64) RaggedExperiment_1.29.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/RaggedExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RaggedExperiment
Bioc Package Browser https://code.bioconductor.org/browse/RaggedExperiment/
Package Short Url https://bioconductor.org/packages/RaggedExperiment/
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