DelayedMatrix-utils: Common operations on DelayedMatrix objects

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

Description

Common operations on DelayedMatrix objects.

Details

In addition to the operations supported on DelayedArray objects, DelayedMatrix objects support the following operations:

Delayed operations:

• t

Block-processed operations:

• rowsum and colsum

• matrix multiplication (%*%) of an ordinary matrix by a DelayedMatrix object

• matrix row/col summarization (see ?`DelayedMatrix-stats`)

See Also

• rowsum in the base package for computing column sums across rows of an ordinary matrix for each level of a grouping variable.

• DelayedArray-utils for common operations on DelayedArray objects.

• DelayedArray-stats for statistical functions on DelayedArray objects.

• DelayedMatrix-stats for DelayedMatrix row/col summarization.

• setAutoRealizationBackend for how to set a automatic realization backend.

• writeHDF5Array in the HDF5Array package for writing an array-like object to an HDF5 file and other low-level utilities to control the location of automatically created HDF5 datasets.

• DelayedArray objects.

• HDF5Array objects in the HDF5Array package.

• array objects in base R.

Examples

## ---------------------------------------------------------------------
## rowsum() / colsum()
## ---------------------------------------------------------------------
library(HDF5Array)
set.seed(123)
m0 <- matrix(runif(14400000), ncol=2250,
             dimnames=list(NULL, sprintf("C%04d", 1:2250)))
M0 <- writeHDF5Array(m0, chunkdim=c(200, 250))
dimnames(M0) <- dimnames(m0)

## --- rowsum() ---

group <- sample(90, nrow(M0), replace=TRUE)  # define groups of rows
rs <- rowsum(M0, group)
rs[1:5, 1:8]
rs2 <- rowsum(M0, group, reorder=FALSE)
rs2[1:5, 1:8]

## Let's see block processing in action:
DelayedArray:::set_verbose_block_processing(TRUE)
setAutoBlockSize(2e6)
rs3 <- rowsum(M0, group)
setAutoBlockSize()
DelayedArray:::set_verbose_block_processing(FALSE)

## Sanity checks:
stopifnot(all.equal(rowsum(m0, group), rs))
stopifnot(all.equal(rowsum(m0, group, reorder=FALSE), rs2))
stopifnot(all.equal(rs, rs3))

## --- colsum() ---

group <- sample(30, ncol(M0), replace=TRUE)  # define groups of cols
cs <- colsum(M0, group)
cs[1:5, 1:7]
cs2 <- colsum(M0, group, reorder=FALSE)
cs2[1:5, 1:7]

## Sanity checks:
stopifnot(all.equal(colsum(m0, group), cs))
stopifnot(all.equal(cs, t(rowsum(t(m0), group))))
stopifnot(all.equal(cs, t(rowsum(t(M0), group))))
stopifnot(all.equal(colsum(m0, group, reorder=FALSE), cs2))
stopifnot(all.equal(cs2, t(rowsum(t(m0), group, reorder=FALSE))))
stopifnot(all.equal(cs2, t(rowsum(t(M0), group, reorder=FALSE))))

## ---------------------------------------------------------------------
## MATRIX MULTIPLICATION
## ---------------------------------------------------------------------
library(HDF5Array)
toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array")
h5ls(toy_h5)
M1 <- HDF5Array(toy_h5, "M1")

## Matrix multiplication is not delayed: the output matrix is realized
## block by block. The current "automatic realization backend" controls
## where realization happens e.g. in memory as an ordinary matrix if not
## (i.e. set to NULL) or in an HDF5 file if set to "HDF5Array".
## See '?setAutoRealizationBackend' for more information about
## "realization backends".
## The output matrix is returned as a DelayedMatrix object with no delayed
## operations on it. The exact class of the object depends on the backend
## e.g. it will be HDF5Matrix with "HDF5Array" backend.

m <- matrix(runif(50000), ncol=nrow(M1))

## Set backend to NULL for in-memory realization:
setAutoRealizationBackend()
P1 <- m %*% M1
P1

## Set backend to HDF5Array for realization in HDF5 file:
setAutoRealizationBackend("HDF5Array")

## With the HDF5Array backend, the output matrix will be written to an
## automatic location on disk:
getHDF5DumpFile()  # HDF5 file where the output matrix will be written
lsHDF5DumpFile()

P2 <- m %*% M1
P2

lsHDF5DumpFile()

## Use setHDF5DumpFile() and setHDF5DumpName() from the HDF5Array package
## to control the location of automatically created HDF5 datasets.

stopifnot(identical(dim(P1), dim(P2)),
          all.equal(as.array(P1), as.array(P2)))

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