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

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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
Date of publication
None
Maintainer
Peter M. Haverty <phaverty@gene.com>
License
Artistic-2.0
Version
1.20.0
URLs

View on Bioconductor

Man pages

annotatedDataFrameFrom
Use BigMatrix in eSet assayData
BigMatrix
Create a new BigMatrix
BigMatrix-class
Class '"BigMatrix"'
BigMatrixFactor
Create a new BigMatrixFactor
BigMatrixFactor-class
Class '"BigMatrixFactor"'
bigmemoryExtras-package
An extension of the bigmemory package with added safety,...
initBigMatrix
Create a new BigMatrix-derived class
updateBackingfiles
Update directory for BigMatrix objects in a collection to new...
updateBigMatrix
Update previous BigMatrix type to new BigMatrix

Files in this package

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