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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bigmemoryExtras")
AuthorPeter M. Haverty
Bioconductor views DataRepresentation Infrastructure
Date of publicationNone
MaintainerPeter M. Haverty <phaverty@gene.com>
LicenseArtistic-2.0
Version1.22.0
https://github.com/phaverty/bigmemoryExtras

View on Bioconductor

Functions

annotatedDataFrameFrom Man page
annotatedDataFrameFrom,BigMatrix-method Man page
apply,BigMatrix-method Man page
as.matrix,BigMatrix-method Man page
BigMatrix Man page
[<-,BigMatrix,ANY,ANY,ANY-method Man page
[,BigMatrix,ANY,ANY,ANY-method Man page
[<-,BigMatrix,ANY,ANY-method Man page
BigMatrix-class Man page
BigMatrixFactor Man page
BigMatrixFactor-class Man page
bigmemoryExtras-package Man page
coerce,BigMatrixFactor,factor-method Man page
coerce,BigMatrixFactor,matrix-method Man page
coerce,BigMatrix,matrix-method Man page
dim,BigMatrix-method Man page
dimnames<-,BigMatrix,ANY-method Man page
dimnames,BigMatrix-method Man page
.initBigMatrix Man page
length,BigMatrix-method Man page
levels<-,BigMatrixFactor-method Man page
levels,BigMatrixFactor-method Man page
ncol,BigMatrix-method Man page
nlevels,BigMatrixFactor-method Man page
nrow,BigMatrix-method Man page
updateBackingfiles Man page
updateBigMatrix Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.