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.

AuthorPeter M. Haverty
Date of publicationNone
MaintainerPeter M. Haverty <phaverty@gene.com>
LicenseArtistic-2.0
Version1.20.0
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

Files

bigmemoryExtras/.BBSoptions
bigmemoryExtras/DESCRIPTION
bigmemoryExtras/NAMESPACE
bigmemoryExtras/R
bigmemoryExtras/R/BigMatrix.R bigmemoryExtras/R/BigMatrixFactor.R bigmemoryExtras/R/collections.R bigmemoryExtras/R/test_bigmemoryExtras_package.R bigmemoryExtras/R/zzz.R
bigmemoryExtras/inst
bigmemoryExtras/inst/NEWS
bigmemoryExtras/inst/TODO
bigmemoryExtras/inst/unitTests
bigmemoryExtras/inst/unitTests/tdata
bigmemoryExtras/inst/unitTests/tdata/ds
bigmemoryExtras/inst/unitTests/tdata/ds.desc.rds
bigmemoryExtras/inst/unitTests/tdata/old.ds.rda
bigmemoryExtras/inst/unitTests/test_BigMatrix.R
bigmemoryExtras/inst/unitTests/test_BigMatrixFactor.R
bigmemoryExtras/man
bigmemoryExtras/man/BigMatrix-class.Rd bigmemoryExtras/man/BigMatrix.Rd bigmemoryExtras/man/BigMatrixFactor-class.Rd bigmemoryExtras/man/BigMatrixFactor.Rd bigmemoryExtras/man/annotatedDataFrameFrom.Rd bigmemoryExtras/man/bigmemoryExtras-package.Rd bigmemoryExtras/man/initBigMatrix.Rd bigmemoryExtras/man/updateBackingfiles.Rd bigmemoryExtras/man/updateBigMatrix.Rd
bigmemoryExtras/tests
bigmemoryExtras/tests/prove.R
bigmemoryExtras/tests/prove.Rout.save
bigmemoryExtras/vignettes
bigmemoryExtras/vignettes/bigmemoryExtras.Rmd

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