bigmemoryExtras

DOI: 10.18129/B9.bioc.bigmemoryExtras    

This package is for version 3.7 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: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("bigmemoryExtras")

Documentation

PDF   Reference Manual
Text   NEWS

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.28.0
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_1.28.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) bigmemoryExtras_1.28.0.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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