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SparseArray

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

Efficient in-memory representation of multidimensional sparse arrays


Bioconductor version: Development (3.19)

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], Jacques Serizay [ctb]

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

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
SparseArray objects HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.3.4
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License Artistic-2.0
Depends R (>= 4.3.0), methods, Matrix, BiocGenerics(>= 0.43.1), MatrixGenerics(>= 1.11.1), S4Vectors, S4Arrays(>= 1.1.6)
Imports stats, matrixStats, IRanges, XVector
System Requirements
URL https://bioconductor.org/packages/SparseArray
Bug Reports https://github.com/Bioconductor/SparseArray/issues
See More
Suggests DelayedArray, testthat, knitr, rmarkdown, BiocStyle
Linking To S4Vectors, IRanges, XVector
Enhances
Depends On Me DelayedArray
Imports Me alabaster.matrix, beachmat
Suggests Me MatrixGenerics, S4Arrays
Links To Me
Build Report Build Report

Package Archives

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

Source Package SparseArray_1.3.4.tar.gz
Windows Binary SparseArray_1.3.4.zip (64-bit only)
macOS Binary (x86_64) SparseArray_1.3.4.tgz
macOS Binary (arm64) SparseArray_1.3.4.tgz
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