RaggedExperiment

This is the development version of RaggedExperiment; for the stable release version, see RaggedExperiment.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-3242-0582 , Lydia King [ctb]

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

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

Martin Morgan, Marcel Ramos. RaggedExperiment: Representation of Sparse Experiments and Assays Across Samples. doi:10.18129/B9.bioc.RaggedExperiment, R package version 1.37.0, https://bioconductor.org/packages/RaggedExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.37.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 4.5.0), GenomicRanges (>= 1.61.1)
Imports	BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment (>= 1.39.1), utils
System Requirements
URL	https://bioconductor.github.io/RaggedExperiment https://bioconductor.org/packages/RaggedExperiment
Bug Reports	https://github.com/Bioconductor/RaggedExperiment/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb, MultiAssayExperiment
Linking To
Enhances
Depends On Me	CNVRanger, curatedPCaData
Imports Me	cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata
Suggests Me	curatedTCGAData, maftools, MultiAssayExperiment, MultiDataSet, SingleCellMultiModal, TENxIO
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	RaggedExperiment_1.37.0.tar.gz
Windows Binary (x86_64)	RaggedExperiment_1.37.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	RaggedExperiment_1.37.0.tgz
macOS Binary (sonoma-arm64)	RaggedExperiment_1.37.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RaggedExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RaggedExperiment
Package Short Url	https://bioconductor.org/packages/RaggedExperiment/
Package Downloads Report	Download Stats