Package: beachmat 2.23.5
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:
beachmat_2.23.5.tar.gz
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beachmat.pdf |beachmat.html✨
beachmat/json (API)
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
On BioConductor:beachmat-2.23.4(bioc 3.21)beachmat-2.22.0(bioc 3.20)
datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp
Last updated 6 days agofrom:747ddb1104. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 16 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 16 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 16 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 16 2024 |
| R-4.4-mac-x86_64 | NOTE | Dec 16 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 16 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 16 2024 |
| R-4.3-mac-x86_64 | NOTE | Dec 16 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 16 2024 |
Exports:checkMemoryCachecolBlockApplyflushMemoryCacheinitializeCppisFileBackedMatrixrealizeFileBackedMatrixrowBlockApplytatami.arithtatami.binarytatami.bindtatami.columntatami.column.nan.countstatami.column.sumstatami.comparetatami.dimtatami.is.sparsetatami.logtatami.logictatami.mathtatami.multiplytatami.nottatami.prefer.rowstatami.realizetatami.roundtatami.rowtatami.row.nan.countstatami.row.sumstatami.subsettatami.transposetoCsparsewhichNonZero
Dependencies:abindassortheadBiocGenericscrayonDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSparseArrayXVectorzlibbioc
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,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 tatami.column.nan.counts tatami.column.sums tatami.compare tatami.dim tatami.is.sparse tatami.log tatami.logic tatami.math tatami.multiply tatami.not tatami.prefer.rows tatami.realize tatami.round tatami.row tatami.row.nan.counts tatami.row.sums tatami.subset tatami.transpose |
| Convert a SparseMatrix to a CsparseMatrix | toCsparse |
| Find non-zero entries of a matrix | whichNonZero |
