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>
citation("bigmemoryExtras")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bigmemoryExtras")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.12), bigmemory (>= 4.5.31) |
| Imports | methods |
| System Requirements | |
| URL | https://github.com/phaverty/bigmemoryExtras |
See More
| Suggests | testthat, BiocGenerics, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | methyAnalysis |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Old Source Packages for BioC 3.13 | Source Archive |