featureCountsParallel: (Alternative) parallel version of 'Rsubread::featureCounts()'

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

(Alternative) parallel version of Rsubread::featureCounts()

Description

Rsubread::featureCounts() already has its own parallel option via the nthreads argument, but sometimes this does not result in a speed-up, presumably due to the file reading being a bottleneck. Instead, this function calls Rsubread::featureCounts() on multiple files in parallel. Empirically, this sometimes results in a better parallel speed-up than using nthreads.

Usage

featureCountsParallel(files, ..., BPPARAM = BiocParallel::bpparam())

Arguments

files	This has the same meaning as in Rsubread::featureCounts()
...	Other arguments are passed to Rsubread::featureCounts()
BPPARAM	A BiocParallelParam instance that determines how to parallelize the operation

Value

See Rsubread::featureCounts().

See Also

Rsubread::featureCounts(), BiocParallel::bplapply()

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.