read_block {DelayedArray} | R Documentation

## Read array blocks

### Description

Use `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 DelayedArray objects but not necessarily).

### Usage

    read_block(x, viewport, as.sparse=FALSE)

### Arguments

`x` | An array-like object, typically a DelayedArray object or derivative.
`viewport` | An ArrayViewport object compatible with `x`, that is, such that `refdim(viewport)` is identical to `dim(x)`.
`as.sparse` | Can be `FALSE`, `TRUE`, or `NA`. If `FALSE` (the default), the block is returned as an ordinary array (a.k.a. dense array). If `TRUE`, it's returned as a SparseArraySeed object. Using `as.sparse=NA` is equivalent to using `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 SparseArraySeed object with numeric or logical data, a block can easily and efficiently be coerced to a sparseMatrix derivative from the Matrix package with `as(block, "sparseMatrix")`. This will return a dgCMatrix object if `type(block)` is `"double"` or `"integer"`, or a lgCMatrix object if it's `"logical"`.

### Value

The data from `x` that belongs to the block delimited by the specified viewport. The data is returned as an ordinary (dense) array or as a SparseArraySeed object. In both cases it has the same dimensions as the `viewport`.

### See Also

- ArrayViewport objects.

- SparseArraySeed objects.

- `write_block`.

- `blockApply` and family for convenient block processing of an array-like object.

- `defaultAutoGrid` and family to generate automatic grids to use for block processing of array-like objects.

- dgCMatrix-class and lgCMatrix-class objects in the Matrix package.

- DelayedArray objects.

- 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))

[Package DelayedArray version 0.16.3 Index]