Package: sparseMatrixStats 1.25.0

Constantin Ahlmann-Eltze

sparseMatrixStats: Summary Statistics for Rows and Columns of Sparse Matrices

High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.

Authors:Constantin Ahlmann-Eltze [aut, cre]

# Install 'sparseMatrixStats' in R:

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

Bug tracker:https://github.com/const-ae/sparsematrixstats/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:sparseMatrixStats-1.25.0(bioc 3.24)sparseMatrixStats-1.24.0(bioc 3.23)

infrastructure software datarepresentation cpp

10.63 score 55 stars 158 packages 326 scripts 72 exports 5 dependencies

Last updated from:9d61c994f4. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	166
linux-devel-arm64	NOTE	173
linux-devel-x86_64	NOTE	212
source / vignettes	OK	252
linux-release-arm64	NOTE	167
linux-release-x86_64	NOTE	236
macos-release-arm64	NOTE	138
macos-release-x86_64	NOTE	285
macos-oldrel-arm64	NOTE	110
macos-oldrel-x86_64	NOTE	251
windows-devel	NOTE	137
windows-release	NOTE	142
windows-oldrel	NOTE	134
wasm-release	OK	150

Exports:colAlls colAnyNAs colAnys colAvgsPerRowSet colCollapse colCounts colCummaxs colCummins colCumprods colCumsums colDiffs colIQRDiffs colIQRs colLogSumExps colMadDiffs colMads colMaxs colMeans2 colMedians colMins colOrderStats colProds colQuantiles colRanges colRanks colSdDiffs colSds colSums2 colTabulates colVarDiffs colVars colWeightedMads colWeightedMeans colWeightedMedians colWeightedSds colWeightedVars rowAlls rowAnyNAs rowAnys rowAvgsPerColSet rowCollapse rowCounts rowCummaxs rowCummins rowCumprods rowCumsums rowDiffs rowIQRDiffs rowIQRs rowLogSumExps rowMadDiffs rowMads rowMaxs rowMeans2 rowMedians rowMins rowOrderStats rowProds rowQuantiles rowRanges rowRanks rowSdDiffs rowSds rowSums2 rowTabulates rowVarDiffs rowVars rowWeightedMads rowWeightedMeans rowWeightedMedians rowWeightedSds rowWeightedVars

Dependencies:lattice Matrix MatrixGenerics matrixStats Rcpp

sparseMatrixStats

Installation | Introduction | Alternative Matrix Creation | Benchmark | Session Info

Rendered fromsparseMatrixStats.Rmdusingknitr::rmarkdown

Last update: 2020-05-10
Started: 2020-04-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if all elements in a row (column) of a matrix-like object are equal to a value	colAlls,xgCMatrix-method rowAlls,xgCMatrix-method
Check if any elements in a row (column) of a matrix-like object is missing	colAnyNAs,xgCMatrix-method rowAnyNAs,xgCMatrix-method
Check if any elements in a row (column) of a matrix-like object is equal to a value	colAnys,xgCMatrix-method rowAnys,xgCMatrix-method
Calculates for each row (column) a summary statistic for equally sized subsets of columns (rows)	colAvgsPerRowSet colAvgsPerRowSet,xgCMatrix-method rowAvgsPerColSet,xgCMatrix-method
Extract one cell from each row (column) of a matrix-like object	colCollapse,xgCMatrix-method rowCollapse,xgCMatrix-method
Count how often an element in a row (column) of a matrix-like object is equal to a value	colCounts,xgCMatrix-method rowCounts,xgCMatrix-method
Calculates the cumulative maxima for each row (column) of a matrix-like object	colCummaxs,dgCMatrix-method rowCummaxs,dgCMatrix-method
Calculates the cumulative minima for each row (column) of a matrix-like object	colCummins,dgCMatrix-method rowCummins,dgCMatrix-method
Calculates the cumulative product for each row (column) of a matrix-like object	colCumprods,xgCMatrix-method rowCumprods,xgCMatrix-method
Calculates the cumulative sum for each row (column) of a matrix-like object	colCumsums,xgCMatrix-method rowCumsums,xgCMatrix-method
Calculates the difference between each element of a row (column) of a matrix-like object	colDiffs,dgCMatrix-method rowDiffs,dgCMatrix-method
Calculates the interquartile range of the difference between each element of a row (column) of a matrix-like object	colIQRDiffs,dgCMatrix-method rowIQRDiffs,dgCMatrix-method
Calculates the interquartile range for each row (column) of a matrix-like object	colIQRs,xgCMatrix-method rowIQRs,xgCMatrix-method
Accurately calculates the logarithm of the sum of exponentials for each row (column) of a matrix-like object	colLogSumExps,xgCMatrix-method rowLogSumExps,xgCMatrix-method
Calculates the mean absolute deviation of the difference between each element of a row (column) of a matrix-like object	colMadDiffs,dgCMatrix-method rowMadDiffs,dgCMatrix-method
Calculates the median absolute deviation for each row (column) of a matrix-like object	colMads,dgCMatrix-method rowMads,dgCMatrix-method
Calculates the maximum for each row (column) of a matrix-like object	colMaxs,dgCMatrix-method rowMaxs,dgCMatrix-method
Calculates the mean for each row (column) of a matrix-like object	colMeans2,xgCMatrix-method rowMeans2,xgCMatrix-method
Calculates the median for each row (column) of a matrix-like object	colMedians,dgCMatrix-method rowMedians,dgCMatrix-method
Calculates the minimum for each row (column) of a matrix-like object	colMins,dgCMatrix-method rowMins,dgCMatrix-method
Calculates an order statistic for each row (column) of a matrix-like object	colOrderStats,dgCMatrix-method rowOrderStats,dgCMatrix-method
Calculates the product for each row (column) in a matrix	colProds,xgCMatrix-method rowProds,xgCMatrix-method
Calculates quantiles for each row (column) of a matrix-like object	colQuantiles,xgCMatrix-method rowQuantiles,xgCMatrix-method
Calculates the minimum and maximum for each row (column) of a matrix-like object	colRanges,dgCMatrix-method rowRanges,dgCMatrix-method
Calculates the rank of the elements for each row (column) of a matrix-like object	colRanks,dgCMatrix-method rowRanks,dgCMatrix-method
Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object	colSdDiffs,dgCMatrix-method rowSdDiffs,dgCMatrix-method
Calculates the standard deviation for each row (column) of a matrix-like object	colSds,xgCMatrix-method rowSds,xgCMatrix-method
Calculates the sum for each row (column) of a matrix-like object	colSums2,xgCMatrix-method rowSums2,xgCMatrix-method
Tabulates the values in a matrix-like object by row (column)	colTabulates,xgCMatrix-method rowTabulates,xgCMatrix-method
Calculates the variance of the difference between each element of a row (column) of a matrix-like object	colVarDiffs,dgCMatrix-method rowVarDiffs,dgCMatrix-method
Calculates the variance for each row (column) of a matrix-like object	colVars,xgCMatrix-method rowVars,xgCMatrix-method
Calculates the weighted median absolute deviation for each row (column) of a matrix-like object	colWeightedMads,dgCMatrix-method rowWeightedMads,dgCMatrix-method
Calculates the weighted mean for each row (column) of a matrix-like object	colWeightedMeans,xgCMatrix-method rowWeightedMeans,xgCMatrix-method
Calculates the weighted median for each row (column) of a matrix-like object	colWeightedMedians,dgCMatrix-method rowWeightedMedians,dgCMatrix-method
Calculates the weighted standard deviation for each row (column) of a matrix-like object	colWeightedSds,xgCMatrix-method rowWeightedSds,xgCMatrix-method
Calculates the weighted variance for each row (column) of a matrix-like object	colWeightedVars,xgCMatrix-method rowWeightedVars,xgCMatrix-method
Union of double and logical column-sparse matrices	xgCMatrix-class