NaArray-matrixStats: NaArray col/row summarization

In Bioconductor/SparseArray: High-performance sparse data representation and manipulation in R

NaArray col/row summarization

Description

EXPERIMENTAL!!!

The SparseArray package provides memory-efficient col/row summarization methods (a.k.a. matrixStats methods) for NaArray objects, like colSums(), rowSums(), colMeans(), rowMeans(), etc...

Note that these are S4 generic functions defined in the MatrixGenerics package, with methods for ordinary matrices defined in the matrixStats package. This man page documents the methods defined for NaArray objects.

IMPORTANT NOTE: This is WORK-IN-PROGRESS! All the col*() methods listed below are supported. However, among the row*() methods, only rowAnyNAs(), rowMins(), rowMaxs(), rowRanges(), rowSums(), and rowSums2() are supported on NaArray objects at the moment.

Usage

## N.B.: Showing ONLY the col*() methods (usage of row*() methods is
## the same):

## S4 method for signature 'NaArray'
colAnyNAs(x, rows=NULL, cols=NULL, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colAnys(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colAlls(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colMins(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colMaxs(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colRanges(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colSums(x, na.rm=FALSE, dims=1)

## S4 method for signature 'NaArray'
colProds(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colMeans(x, na.rm=FALSE, dims=1)

## S4 method for signature 'NaArray'
colSums2(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colMeans2(x, rows=NULL, cols=NULL, na.rm=FALSE, dims=1, ..., useNames=NA)

## S4 method for signature 'NaArray'
colVars(x, rows=NULL, cols=NULL, na.rm=FALSE, center=NULL, dims=1,
           ..., useNames=NA)

## S4 method for signature 'NaArray'
colSds(x, rows=NULL, cols=NULL, na.rm=FALSE, center=NULL, dims=1,
          ..., useNames=NA)

Arguments

x	An NaMatrix or NaArray object.
rows, cols, ...	Not supported.
na.rm, useNames, center	See man pages of the corresponding generics in the MatrixGenerics package (e.g. ?MatrixGenerics::colVars) for a description of these arguments. Note that, unlike the methods for ordinary matrices defined in the matrixStats package, the center argument of the colVars(), rowVars(), colSds(), and rowSds() methods for SparseArray objects can only be a single value (or a NULL). In particular, if x has more than one column, then center cannot be a vector with one value per column in x.
dims	See ?base::colSums for a description of this argument.

Details

These methods are typically used with na.rm=TRUE when called on an NaMatrix or NaArray object.

All these methods operate natively on the NaArray internal representation, for maximum efficiency.

Note that more col/row summarization methods might be added in the future.

Value

See man pages of the corresponding generics in the MatrixGenerics package (e.g. ?MatrixGenerics::colRanges) for the value returned by these methods.

Note

Most col*() methods for NaArray objects are multithreaded. See set_SparseArray_nthread for how to control the number of threads.

See Also

• NaArray objects.

• The man pages of the various generic functions defined in the MatrixGenerics package e.g. MatrixGenerics::colVars etc...

Examples

# COMING SOON...

Bioconductor/SparseArray documentation built on Nov. 14, 2024, 6:22 p.m.