bigmemoryExtras

DOI: 10.18129/B9.bioc.bigmemoryExtras    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see bigmemoryExtras.

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

Bioconductor version: 3.13

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 "4.1") 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

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (9 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	methyAnalysis
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/bigmemoryExtras/
Package Downloads Report	Download Stats