Overview | Linking instructions | Reading matrix data | Enabling parallelization | Comparison to block processing | Session information
Package: beachmat 2.29.3
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:
beachmat_2.29.3.tar.gz
beachmat_2.29.3.zip(r-4.7-x86_64)beachmat_2.29.3.zip(r-4.7-arm64)beachmat_2.29.3.zip(r-4.6-x86_64)beachmat_2.29.3.zip(r-4.6-arm64)beachmat_2.29.3.zip(r-4.5-x86_64)
beachmat_2.29.3.tgz(r-4.6-x86_64)beachmat_2.29.3.tgz(r-4.6-arm64)beachmat_2.29.3.tgz(r-4.5-x86_64)beachmat_2.29.3.tgz(r-4.5-arm64)
beachmat_2.29.3.tar.gz(r-4.7-arm64)beachmat_2.29.3.tar.gz(r-4.7-x86_64)beachmat_2.29.3.tar.gz(r-4.6-arm64)beachmat_2.29.3.tar.gz(r-4.6-x86_64)
beachmat_2.29.3.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
On BioConductor:beachmat-2.29.3(bioc 3.24)beachmat-2.28.0(bioc 3.23)
datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp
Last updated from:7fe7dc234e. Checks:1 WARNING, 13 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 389 | ||
| linux-devel-arm64 | NOTE | 419 | ||
| linux-devel-x86_64 | NOTE | 570 | ||
| source / vignettes | OK | 560 | ||
| linux-release-arm64 | NOTE | 515 | ||
| linux-release-x86_64 | NOTE | 692 | ||
| macos-release-arm64 | NOTE | 362 | ||
| macos-release-x86_64 | NOTE | 880 | ||
| macos-oldrel-arm64 | NOTE | 412 | ||
| macos-oldrel-x86_64 | NOTE | 686 | ||
| windows-devel-arm64 | NOTE | 557 | ||
| windows-devel-x86_64 | NOTE | 535 | ||
| windows-release-arm64 | NOTE | 533 | ||
| windows-release-x86_64 | NOTE | 712 | ||
| windows-oldrel-x86_64 | NOTE | 421 | ||
| wasm-release | OK | 290 |
Exports:checkMemoryCachecolBlockApplyflushMemoryCachegetExecutorinitializeCppisFileBackedMatrixrealizeFileBackedMatrixrowBlockApplytatami.arithtatami.binarytatami.bindtatami.columntatami.column.medianstatami.column.nan.countstatami.column.sumstatami.comparetatami.dimtatami.gettatami.is.sparsetatami.logtatami.logictatami.mathtatami.medianstatami.multiplytatami.nan.countstatami.nottatami.prefer.rowstatami.realizetatami.roundtatami.rowtatami.row.medianstatami.row.nan.countstatami.row.sumstatami.subsettatami.sumstatami.sums.by.grouptatami.transposetatami.variancestoCsparsewhichNonZero
Dependencies:abindassortheadBiocGenericsDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSparseArrayXVector
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 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 tatami.variances |
| Convert a SparseMatrix to a CsparseMatrix | toCsparse |
| Find non-zero entries of a matrix | whichNonZero |