Package: beachmat 2.21.3

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]

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NEWS

# 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-2.21.3(bioc 3.20)beachmat-2.20.0(bioc 3.19)

bioconductor-package

9 exports 6.86 score 15 dependencies 130 dependents 3 mentions

Last updated 1 months agofrom:a432503820

Exports:checkMemoryCache colBlockApply flushMemoryCache initializeCpp isFileBackedMatrix realizeFileBackedMatrix rowBlockApply toCsparse whichNonZero

Dependencies:abind BiocGenerics crayon DelayedArray IRanges lattice Matrix MatrixGenerics matrixStats Rcpp S4Arrays S4Vectors SparseArray XVector zlibbioc

Developing packages with beachmat

Aaron Lun

Rendered fromlinking.Rmdusingknitr::rmarkdownon Jul 03 2024.

Last update: 2023-07-05
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
Initialize matrix in C++ memory space	initializeCpp initializeCpp,ANY-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
Convert a SparseArraySeed to a CsparseMatrix	toCsparse
Find non-zero entries of a matrix	whichNonZero whichNonZero,ANY-method whichNonZero,CsparseMatrix-method whichNonZero,DelayedMatrix-method whichNonZero,SparseArraySeed-method whichNonZero,TsparseMatrix-method