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\name{read_block}
\alias{read_block}
\alias{read_block,ANY-method}
\alias{is_sparse}
\alias{read_sparse_block}
\alias{read_sparse_block,ANY-method}
\alias{read_sparse_block,SparseArraySeed-method}
\title{Read array blocks}
\description{
Use \code{read_block} to read a block from an array-like object.
The function is typically used in the context of block processing
of array-like objects (typically \link{DelayedArray} objects but
not necessarily).
}
\usage{
read_block(x, viewport, as.sparse=FALSE)
}
\arguments{
\item{x}{
An array-like object, typically a \link{DelayedArray} object
or derivative.
}
\item{viewport}{
An \link{ArrayViewport} object compatible with \code{x}, that is,
such that \code{refdim(viewport)} is identical to \code{dim(x)}.
}
\item{as.sparse}{
Can be \code{FALSE}, \code{TRUE}, or \code{NA}.
If \code{FALSE} (the default), the block is returned as an ordinary
array (a.k.a. dense array). If \code{TRUE}, it's returned as a
\link{SparseArraySeed} object. Using \code{as.sparse=NA} is equivalent
to using \code{as.sparse=is_sparse(x)} and is the most efficient way
to read a block. (This might become the default in the future.)
Note that when returned as a 2D \link{SparseArraySeed} object with
numeric or logical data, a block can easily and efficiently
be coerced to a \link[Matrix]{sparseMatrix} derivative from the
\pkg{Matrix} package with \code{as(block, "sparseMatrix")}.
This will return a dgCMatrix object if \code{type(block)}
is \code{"double"} or \code{"integer"}, or a lgCMatrix
object if it's \code{"logical"}.
}
}
\value{
The data from \code{x} that belongs to the block delimited by the
specified viewport. The data is returned as an ordinary (dense) array
or as a \link{SparseArraySeed} object. In both cases it has the same
dimensions as the \code{viewport}.
}
\seealso{
\itemize{
\item \link{ArrayViewport} objects.
\item \link{SparseArraySeed} objects.
\item \code{\link{write_block}}.
\item \code{\link{blockApply}} and family for convenient block
processing of an array-like object.
\item \code{\link{defaultAutoGrid}} and family to create automatic
grids to use for block processing of array-like objects.
\item \link[Matrix]{dgCMatrix-class} and \link[Matrix]{lgCMatrix-class}
objects in the \pkg{Matrix} package.
\item \link{DelayedArray} objects.
\item \link[base]{array} objects in base R.
}
}
\examples{
## ---------------------------------------------------------------------
## TYPICAL USE
## ---------------------------------------------------------------------
## read_block() is typically used in combination with write_block().
## See '?write_block' for typical uses of the read_block/write_block
## combo.
## ---------------------------------------------------------------------
## VERY BASIC (BUT ALSO VERY ARTIFICIAL) EXAMPLE 1:
## Read a block from an ordinary matrix
## ---------------------------------------------------------------------
m1 <- matrix(1:30, ncol=5)
m1
## Define the viewport on 'm1' to read the data from:
block1_dim <- c(4, 3)
viewport1 <- ArrayViewport(dim(m1), IRanges(c(3, 2), width=block1_dim))
viewport1
## Read the block:
block1 <- read_block(m1, viewport1) # same as m1[3:6, 2:4, drop=FALSE]
block1
## Sanity checks:
stopifnot(identical(dim(viewport1), dim(block1)))
stopifnot(identical(m1[3:6, 2:4, drop=FALSE], block1))
## ---------------------------------------------------------------------
## VERY BASIC (BUT ALSO VERY ARTIFICIAL) EXAMPLE 2:
## Read a block from a sparse matrix
## ---------------------------------------------------------------------
m2 <- rsparsematrix(12, 20, density=0.2,
rand.x=function(n) sample(25, n, replace=TRUE))
m2
## Define the viewport on 'm2' to read the data from:
block2_dim <- c(2, 20)
viewport2 <- ArrayViewport(dim(m2), IRanges(c(1, 1), width=block2_dim))
viewport2
## By default, read_block() always returns an ordinary matrix or array:
block2 <- read_block(m2, viewport2)
block2
## It is recommended to use 'as.sparse=NA' rather than 'as.sparse=TRUE'
## or 'as.sparse=FALSE' to let read_block() pick up the optimal
## representation:
block2b <- read_block(m2, viewport2, as.sparse=NA)
class(block2b) # a SparseArraySeed object
as(block2b, "sparseMatrix")
## For comparison, using 'as.sparse=NA' on 'm1' still returns the
## block as an ordinary matrix (a.k.a. dense matrix):
read_block(m1, viewport1, as.sparse=NA)
## Sanity checks:
stopifnot(identical(dim(viewport2), dim(block2)))
stopifnot(identical(dim(viewport2), dim(block2b)))
stopifnot(identical(block2, as.array(block2b)))
## ---------------------------------------------------------------------
## VERY BASIC (BUT ALSO VERY ARTIFICIAL) EXAMPLE 3:
## Read a block from a 3D array
## ---------------------------------------------------------------------
a3 <- array(1:60, 5:3)
## Define the viewport on 'a3' to read the data from:
block3_dim <- c(2, 4, 1)
viewport3 <- ArrayViewport(dim(a3), IRanges(c(1, 1, 3), width=block3_dim))
viewport3
## Read the block:
block3 <- read_block(a3, viewport3) # same as a3[1:2, 1:4, 3, drop=FALSE]
block3
## Note that unlike [, read_block() never drops dimensions.
## Sanity checks:
stopifnot(identical(dim(viewport3), dim(block3)))
stopifnot(identical(a3[1:2, 1:4, 3, drop=FALSE], block3))
}
\keyword{methods}
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