bigmemoryExtras

DOI: 10.18129/B9.bioc.bigmemoryExtras    

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

Bioconductor version: Release (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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("bigmemoryExtras", version = "3.8")

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 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/
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