Package: DelayedMatrixStats 1.29.0

Peter Hickey

DelayedMatrixStats: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects

A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

Authors:Peter Hickey [aut, cre], Hervé Pagès [ctb], Aaron Lun [ctb]

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NEWS

# Install 'DelayedMatrixStats' in R:

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

Bug tracker:https://github.com/petehaitch/delayedmatrixstats/issues

On BioConductor:DelayedMatrixStats-1.29.0(bioc 3.21)DelayedMatrixStats-1.28.0(bioc 3.20)

infrastructure datarepresentation software

11.77 score 15 stars 114 packages 203 scripts 28k downloads 1 mentions 72 exports 17 dependencies

Last updated 2 months agofrom:bfe5e8b24f. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 27 2024
R-4.5-win	NOTE	Nov 27 2024
R-4.5-linux	NOTE	Nov 27 2024
R-4.4-win	NOTE	Nov 27 2024
R-4.4-mac	NOTE	Nov 27 2024
R-4.3-win	NOTE	Nov 27 2024
R-4.3-mac	NOTE	Nov 27 2024

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

Overview of DelayedMatrixStats

Peter Hickey

Rendered fromDelayedMatrixStatsOverview.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2023-10-12
Started: 2017-10-05

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