bigmemoryExtras

DOI: 10.18129/B9.bioc.bigmemoryExtras    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see bigmemoryExtras.

An extension of the bigmemory package with added safety, convenience, and a factor class

Bioconductor version: 3.8

This package defines a "BigMatrix" ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. We provide utilities for using BigMatrix-derived classes as assayData matrices within the Biobase package's eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a "BigMatrixFactor" class, a file-backed matrix with factor properties.

Author: Peter M. Haverty

Maintainer: Peter M. Haverty <phaverty at gene.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("bigmemoryExtras")

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

Documentation

PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.30.0
In Bioconductor since	BioC 2.11 (R-2.15) (6.5 years)
License	Artistic-2.0
Depends	R (>= 2.12), bigmemory (>= 4.5.31)
Imports	methods
LinkingTo
Suggests	testthat, BiocGenerics, BiocStyle, knitr
SystemRequirements
Enhances
URL	https://github.com/phaverty/bigmemoryExtras
Depends On Me
Imports Me	gCMAP
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bigmemoryExtras_1.30.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	bigmemoryExtras_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bigmemoryExtras
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bigmemoryExtras
Package Short Url	http://bioconductor.org/packages/bigmemoryExtras/
Package Downloads Report	Download Stats