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GSVA version there was a parallel.sz parameter for defining this, but in the new API I feel lost, as that parameter is no longer valid.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)

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.