bpplapply: Wrapper for bplapply

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Wrapper for bplapply

Description

Wrapper function for bplapply that automatically handles issues with BiocParallel related to different OS platforms.

Usage

bpplapply(
  X,
  FUN,
  apply_fun = parallel::mclapply,
  workers = check_workers(),
  progressbar = workers > 1,
  verbose = workers == 1,
  use_snowparam = TRUE,
  register_now = 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	Iterator function to use.
workers	Number of threads to parallelize across.
progressbar	logical(1) Enable progress bar (based on plyr:::progress_text).
verbose	Print messages.
use_snowparam	Whether to use SnowParam (default: TRUE) or MulticoreParam (FALSE) when parallelising across multiple workers.
register_now	Register the cores now with register (TRUE), or simply return the BPPARAM object (default: FALSE).
...	Arguments passed on to BiocParallel::bplapply 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.

Value

(Named) list.

Examples

X <- stats::setNames(seq_len(length(letters)), letters)
out <- bpplapply(X, print) 

neurogenomics/EpiCompare documentation built on Oct. 18, 2024, 11:04 p.m.