chunk_apply {matter}R Documentation

Apply Functions Over Chunks of a List, Vector, or Matrix

Description

Perform equivalents of apply, lapply, and mapply, but over parallelized chunks of the data. This is most useful if accessing the data is potentially time-consuming, such as for file-based matter objects. Operating on chunks reduces the number of I/O operations.

Usage

chunk_apply(X, FUN, MARGIN, ..., simplify = FALSE,
    chunks = NA, view = c("element", "chunk"),
    attr = list(), alist = list(), pattern = NULL,
    outfile = NULL, verbose = FALSE,
    BPREDO = list(), BPPARAM = bpparam())

chunk_mapply(FUN, ..., MoreArgs = NULL, simplify = FALSE,
    chunks = NA, view = c("element", "chunk"),
    attr = list(), alist = list(), pattern = NULL,
    outfile = NULL, verbose = FALSE,
    BPREDO = list(), BPPARAM = bpparam())

Arguments

X

A list, vector, or matrix for chunk_apply(). These may be any class that implements suitable methods for [, [[, dim, and length(). Only lists are supported for chunk_mapply().

FUN

The function to be applied.

MARGIN

If the object is matrix-like, which dimension to iterate over. Must be 1 or 2, where 1 indicates rows and 2 indicates columns. The dimension names can also be used if X has dimnames set.

MoreArgs

A list of other arguments to FUN.

...

Additional arguments to be passed to FUN.

simplify

Should the result be simplified into a vector, matrix, or higher dimensional array?

chunks

The number of chunks to use. If NA (the default), this is inferred from chunksize(X) for matter objects, or from getOption("matter.default.chunksize") for non-matter classes. For IO-bound operations, using fewer chunks will often be faster, but use more memory.

view

What should be passed as the argment to FUN: "element" means the vector element, row, or column are passed (same as the behavior of lapply and apply), and "chunk" means to pass the entire chunk.

attr

A named list of attributes that will be attached to the argument passed to FUN as-is.

alist

A named list of vector-like attributes that will be attached to the argument passed to FUN, subsetted to the current elements. Typically, each attribute should be as long as X, unless pattern is specified, in which case each attribute should be as long as pattern.

pattern

A list of indices giving a pattern over which to apply FUN to X. Each element of pattern should give a vector of indices which can be used subscript X. For time and space efficiency, no attempt is made to verify these indices are valid.

outfile

If non-NULL, a file path where the results should be written as they are processed. If specified, FUN must return a 'raw', 'logical', 'integer', or 'numeric' vector. The result will be returned as a matter object.

verbose

Should user messages be printed with the current chunk being processed?

BPREDO

See documentation for bplapply.

BPPARAM

An optional instance of BiocParallelParam. See documentation for bplapply.

Value

Typically, a list if simplify=FALSE. Otherwise, the results may be coerced to a vector or array.

Author(s)

Kylie A. Bemis

See Also

apply, lapply, mapply,

Examples

register(SerialParam())

set.seed(1)
x <- matrix(rnorm(1000^2), nrow=1000, ncol=1000)

out <- chunk_apply(x, mean, 1, chunks=20, verbose=TRUE)

[Package matter version 1.13.8 Index]