R: Parallel, vectorized evaluation

bpvec {BiocParallel}

R Documentation

Parallel, vectorized evaluation

Description

bpvec applies FUN to subsets of X. Any type of object X is allowed, provided length, [, and c methods are available. The return value is a vector of length equal to X, as with FUN(X).

Usage

bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())

## S4 method for signature 'ANY,ANY'
bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())

## S4 method for signature 'ANY,BiocParallelParam'
bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())

## S4 method for signature 'ANY,missing'
bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())

Arguments

`X`	Any object for which methods `length`, `[`, and `c` are implemented.
`FUN`	The `function` to be applied to subsets of `X`.
`...`	Additional arguments for `FUN`.
`AGGREGATE`	A function taking any number of arguments `...` called to reduce results (elements of the `...` argument of `AGGREGATE` from parallel jobs. The default, `c`, concatenates objects and is appropriate for vectors; `rbind` might be appropriate for data frames.
`BPPARAM`	A optional `BiocParallelParam` instance determining the parallel back-end to be used during evaluation.

Details

When BPPARAM is an instance of a class derived from BiocParallelParam for which no other method applies, this method creates a vector of indexes and uses these in conjunction with bplapply to arrange for parallel evaluation.

When BPPARAM is a class for which no method is defined (e.g., SerialParam), FUN(X) is used.

See showMethods{bpvec} for additional methods, e.g., method?bpvec("MulticoreParam").

Value

The result should be identical to FUN(X, ...) (assuming that AGGREGATE is set appropriately).

Author(s)

Martin Morgan mailto:mtmorgan@fhcrc.org. Original code as attributed in pvec.

Examples

showMethods("bpvec")

## ten tasks (1:10), called with as many back-end elements are specified
## by BPPARAM.  Compare with bplapply
system.time(result <- bpvec(1:10, function(v) {
    message("working") ## 10 tasks
    sqrt(v)
}))
result

[Package BiocParallel version 0.6.1 Index]