GSVA 1.52.2 (new API) nb of workers?
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@466b49a7
Last seen 4 days ago
France

Hello, thanks for the latest GSVA ! I was wondering how to be able to use all my PC cores (workers=8): in the older GSVA version there was a parallel.sz parameter for defining this, but in the new API I feel lost, as that parameter is no longer valid. Here my code with the new API:

gsvaPar <- gsvaParam(
    exprData=as.matrix(expression),
    geneSets=pathways_list,
    minSize = 5,
    kcdf = "Gaussian")

result <- GSVA::gsva(
  gsvaPar, verbose=TRUE)
parallelize workers GSVA • 82 views
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Axel Klenk ★ 1.0k
@axel-klenk-3224
Last seen 10 hours ago
UPF, Barcelona, Spain

Hello, and thanks for using GSVA!

For quite some time GSVA is supporting Bioconductor's own BiocParallel framework and argument parallel.sz has finally been discontinued to avoid duplication (and potential confusion). To execute gsva(.) in parallel, simply change your code to e.g.:

result <- gsva(gsvaPar, verbose=TRUE, BPPARAM=MulticoreParam(workers=8))

The example above is using MulticoreParam(.) for forked processes on multicore CPUs. Please see the BiocParallel documentation and vignette for more information.

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