sparseMatrix-utils: sparseMatrix utilities

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

Description

Some utilities to operate natively on sparseMatrix objects (e.g. dgCMatrix and lgCMatrix objects) from the Matrix package. Mostly for internal use by the DelayedArray package.

Usage

## rowsum() and colsum() S4 generics:

#rowsum(x, group, reorder=TRUE, ...)
#colsum(x, group, reorder=TRUE, ...)

## Default methods:

## S4 method for signature 'ANY'
rowsum(x, group, reorder=TRUE, ...)
## S4 method for signature 'ANY'
colsum(x, group, reorder=TRUE, ...)

## rowsum() method for dgCMatrix objects:

## S4 method for signature 'dgCMatrix'
rowsum(x, group, reorder=TRUE, ...)

Arguments

x	A numeric matrix-like object.
group, reorder, ...	See ?base::rowsum for a description of these arguments.

Value

See ?base::rowsum for the value returned by the default rowsum method.

The default colsum method returns t(rowsum(t(x), group, reorder=reorder, ...)).

See Also

• DelayedMatrix-utils in this package for the rowsum and colsum methods defined for DelayedMatrix objects.

• base::rowsum in the base package for the default rowsum method.

• dgCMatrix objects in the Matrix package.

Examples

m0 <- rsparsematrix(1e5, 800, density=0.15)  # sparse representation
m <- as.matrix(m0)                           # dense representation
group <- sample(20, nrow(m), replace=TRUE)

## 'rowsum(m0)' is about 4x faster than 'rowsum(m)':
rs0 <- rowsum(m0, group)
rs <- rowsum(m, group)

stopifnot(identical(rs0, rs))

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