Use BiocParallel functions with appropriate parameters

Light wrapper around BiocParallel functions that automatically sets the appropriate parameters based on the number of workers specified.

Usage

bpapply(
  X,
  FUN,
  apply_fun = BiocParallel::bplapply,
  workers = 1,
  progressbar = FALSE,
  force_snowparam = FALSE,
  verbose = FALSE,
  ...
)

Arguments

X

Any object for which methods length, [, and [[ are implemented.

FUN

The function to be applied to each element of X.

apply_fun

A BiocParallel function to use for parallel processing. (default = BiocParallel::bplapply)

workers

The number of workers to use for parallel processing.

progressbar

logical(1) Enable progress bar (based on plyr:::progress_text).

force_snowparam

A logical indicating whether to force the use of SnowParam object.

verbose

A logical indicating whether to print verbose messages while running the function. (default = FALSE)

...

Arguments passed on to BiocParallel::bplapply, BiocParallel::bpmapply

BPPARAM

An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to BiocParallel functions.

BPREDO

A list of output from bplapply with one or more failed elements. When a list is given in BPREDO, bpok is used to identify errors, tasks are rerun and inserted into the original results.

BPOPTIONS

Additional options to control the behavior of the parallel evaluation, see bpoptions.

MoreArgs

List of additional arguments to FUN.

SIMPLIFY

If TRUE the result will be simplified using simplify2array.

USE.NAMES

If TRUE the result will be named.

Value

Output relevant to the apply_fun specified.

Examples

half_it <- function(arg1) return(arg1 / 2)
x <- seq_len(10)

res <- bpapply(x, half_it, workers = 2)
print(res)
#> [[1]]
#> [1] 0.5
#> 
#> [[2]]
#> [1] 1
#> 
#> [[3]]
#> [1] 1.5
#> 
#> [[4]]
#> [1] 2
#> 
#> [[5]]
#> [1] 2.5
#> 
#> [[6]]
#> [1] 3
#> 
#> [[7]]
#> [1] 3.5
#> 
#> [[8]]
#> [1] 4
#> 
#> [[9]]
#> [1] 4.5
#> 
#> [[10]]
#> [1] 5
#>