DelayedMatrix-stats: DelayedMatrix row/col summarization

In DelayedArray: A unified framework for working transparently with on-disk and in-memory array-like datasets

Description

Only a small number of row/col summarization methods are provided by the DelayedArray package.

See the DelayedMatrixStats package for an extensive set of row/col summarization methods.

Usage

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

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

## S4 method for signature 'DelayedMatrix'
rowMins(x, rows=NULL, cols=NULL, na.rm=FALSE)
## S4 method for signature 'DelayedMatrix'
colMins(x, rows=NULL, cols=NULL, na.rm=FALSE)

## S4 method for signature 'DelayedMatrix'
rowMaxs(x, rows=NULL, cols=NULL, na.rm=FALSE)
## S4 method for signature 'DelayedMatrix'
colMaxs(x, rows=NULL, cols=NULL, na.rm=FALSE)

## S4 method for signature 'DelayedMatrix'
rowRanges(x, rows=NULL, cols=NULL, na.rm=FALSE)
## S4 method for signature 'DelayedMatrix'
colRanges(x, rows=NULL, cols=NULL, na.rm=FALSE)

Arguments

x	A DelayedMatrix object.
na.rm	Should missing values (including NaN) be omitted from the calculations?
dims, rows, cols	These arguments are not supported. Don't use them.

Details

All these operations are block-processed.

See Also

• The DelayedMatrixStats package for more row/col summarization methods for DelayedMatrix objects.

• rowSums in the base package and rowMaxs in the matrixStats package for row/col summarization of an ordinary matrix.

• DelayedMatrix-utils for other common operations on DelayedMatrix objects.

• DelayedMatrix objects.

• matrix objects in base R.

Examples

library(HDF5Array)
toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array")
h5ls(toy_h5)

M1 <- HDF5Array(toy_h5, "M1")
M2 <- HDF5Array(toy_h5, "M2")

M12 <- rbind(M1, t(M2))        # delayed

## All these operations are block-processed.

rowSums(M12)
colSums(M12)

rowMeans(M12)
colMeans(M12)

rmins <- rowMins(M12)
cmins <- colMins(M12)

rmaxs <- rowMaxs(M12)
cmaxs <- colMaxs(M12)

rranges <- rowRanges(M12)
cranges <- colRanges(M12)

## Sanity checks:
m12 <- rbind(as.matrix(M1), t(as.matrix(M2)))
stopifnot(identical(rowSums(M12), rowSums(m12)))
stopifnot(identical(colSums(M12), colSums(m12)))
stopifnot(identical(rowMeans(M12), rowMeans(m12)))
stopifnot(identical(colMeans(M12), colMeans(m12)))
stopifnot(identical(rmins, rowMins(m12)))
stopifnot(identical(cmins, colMins(m12)))
stopifnot(identical(rmaxs, rowMaxs(m12)))
stopifnot(identical(cmaxs, colMaxs(m12)))
stopifnot(identical(rranges, cbind(rmins, rmaxs, deparse.level=0)))
stopifnot(identical(cranges, cbind(cmins, cmaxs, deparse.level=0)))

DelayedArray documentation built on March 25, 2021, 6:01 p.m.