SparseArray

DOI: 10.18129/B9.bioc.SparseArray  

Efficient in-memory representation of multidimensional sparse arrays

Bioconductor version: Release (3.17)

The SparseArray package is an infrastructure package that provides an array-like container for efficient in-memory representation of multidimensional sparse data in R. The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data, the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.

Author: Hervé Pagès [aut, cre], Vince Carey [fnd], Rafael A. Irizarry [fnd]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Installation

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

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

BiocManager::install("SparseArray")

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("SparseArray")

 

HTML	R Script	SparseArray objects
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.0.12
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.3.0), methods, Matrix, BiocGenerics(>= 0.43.1), MatrixGenerics(>= 1.11.1), S4Vectors, S4Arrays(>= 1.0.6)
Imports	stats, matrixStats, IRanges, XVector
LinkingTo	S4Vectors, IRanges, XVector
Suggests	DelayedArray, testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/SparseArray
BugReports	https://github.com/Bioconductor/SparseArray/issues
Depends On Me
Imports Me
Suggests Me	MatrixGenerics, S4Arrays
Links To Me
Build Report

Package Archives

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

Source Package	SparseArray_1.0.12.tar.gz
Windows Binary	SparseArray_1.0.12.zip
macOS Binary (x86_64)	SparseArray_1.0.12.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SparseArray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SparseArray
Bioc Package Browser	https://code.bioconductor.org/browse/SparseArray/
Package Short Url	https://bioconductor.org/packages/SparseArray/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive