Package: beachmat 2.29.0

Aaron Lun

beachmat: Compiling Bioconductor to Handle Each Matrix Type

Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.

Authors:Aaron Lun [aut, cre], Hervé Pagès [aut], Mike Smith [aut]

beachmat_2.29.0.tar.gz
beachmat_2.29.0.zip(r-4.7)beachmat_2.29.0.zip(r-4.6)beachmat_2.29.0.zip(r-4.5)
beachmat_2.29.0.tgz(r-4.6-x86_64)beachmat_2.29.0.tgz(r-4.6-arm64)beachmat_2.29.0.tgz(r-4.5-x86_64)beachmat_2.29.0.tgz(r-4.5-arm64)
beachmat_2.29.0.tar.gz(r-4.7-arm64)beachmat_2.29.0.tar.gz(r-4.7-x86_64)beachmat_2.29.0.tar.gz(r-4.6-arm64)beachmat_2.29.0.tar.gz(r-4.6-x86_64)
beachmat_2.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
beachmat/json (API)

# Install 'beachmat' in R:

install.packages('beachmat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tatami-inc/beachmat/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:beachmat-2.29.0(bioc 3.24)beachmat-2.28.0(bioc 3.23)

datarepresentation dataimport infrastructure bioconductor-package human-cell-atlas matrix-library cpp

9.71 score 5 stars 195 packages 26 scripts 3 mentions 39 exports 15 dependencies

Last updated from:de69b77e7c. Checks:12 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	542
linux-devel-arm64	WARNING	685
linux-devel-x86_64	WARNING	772
source / vignettes	OK	755
linux-release-arm64	WARNING	682
linux-release-x86_64	WARNING	812
macos-release-arm64	WARNING	284
macos-release-x86_64	WARNING	565
macos-oldrel-arm64	WARNING	366
macos-oldrel-x86_64	WARNING	1342
windows-devel	WARNING	471
windows-release	WARNING	515
windows-oldrel	WARNING	477
wasm-release	OK	266

Exports:checkMemoryCache colBlockApply flushMemoryCache getExecutor initializeCpp isFileBackedMatrix realizeFileBackedMatrix rowBlockApply tatami.arith tatami.binary tatami.bind tatami.column tatami.column.medians tatami.column.nan.counts tatami.column.sums tatami.compare tatami.dim tatami.get tatami.is.sparse tatami.log tatami.logic tatami.math tatami.medians tatami.multiply tatami.nan.counts tatami.not tatami.prefer.rows tatami.realize tatami.round tatami.row tatami.row.medians tatami.row.nan.counts tatami.row.sums tatami.subset tatami.sums tatami.sums.by.group tatami.transpose toCsparse whichNonZero

Dependencies:abind assorthead BiocGenerics DelayedArray generics IRanges lattice Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors SparseArray XVector

Developing packages with beachmat

Rendered fromlinking.Rmdusingknitr::rmarkdown

Last update: 2025-08-19
Started: 2018-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check the in-memory cache for matrix instances	checkMemoryCache flushMemoryCache
Apply over blocks of columns or rows	colBlockApply rowBlockApply
Get the parallel executor	getExecutor
Initialize matrix in C++ memory space	initializeCpp initializeCpp,ANY-method initializeCpp,ConstantArraySeed-method initializeCpp,DelayedAbind-method initializeCpp,DelayedAperm-method initializeCpp,DelayedMatrix-method initializeCpp,DelayedNaryIsoOp-method initializeCpp,DelayedSetDimnames-method initializeCpp,DelayedSubset-method initializeCpp,DelayedUnaryIsoOpStack-method initializeCpp,DelayedUnaryIsoOpWithArgs-method initializeCpp,dgCMatrix-method initializeCpp,dgeMatrix-method initializeCpp,dgRMatrix-method initializeCpp,externalptr-method initializeCpp,lgCMatrix-method initializeCpp,lgeMatrix-method initializeCpp,lgRMatrix-method initializeCpp,matrix-method initializeCpp,SVT_SparseMatrix-method
Realize a file-backed DelayedMatrix	isFileBackedMatrix realizeFileBackedMatrix
Tatami utilities	tatami-utils tatami.arith tatami.binary tatami.bind tatami.column.medians tatami.column.nan.counts tatami.column.sums tatami.compare tatami.dim tatami.get tatami.is.sparse tatami.log tatami.logic tatami.math tatami.medians tatami.multiply tatami.nan.counts tatami.not tatami.prefer.rows tatami.realize tatami.round tatami.row.medians tatami.row.nan.counts tatami.row.sums tatami.subset tatami.sums tatami.sums.by.group tatami.transpose
Convert a SparseMatrix to a CsparseMatrix	toCsparse
Find non-zero entries of a matrix	whichNonZero