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RaggedExperiment

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

Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: Development (3.18)

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 roswellpark.org>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
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

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.25.1
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 4.2.0), GenomicRanges(>= 1.37.17)
Imports BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
System Requirements
Enhances
URL
Bug Reports https://github.com/Bioconductor/RaggedExperiment/issues
See More
Depends On Me CNVRanger, compartmap
Imports Me cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata
Suggests Me curatedTCGAData, maftools, MultiAssayExperiment, MultiDataSet, SingleCellMultiModal, TENxIO
Links To Me
Build Report  

Package Archives

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

Source Package RaggedExperiment_1.25.1.tar.gz
Windows Binary RaggedExperiment_1.25.1.zip
macOS Binary (x86_64) RaggedExperiment_1.25.1.tgz
macOS Binary (arm64) RaggedExperiment_1.25.1.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/
Package Downloads Report Download Stats