Extends the functionality of fgsea::fgsea().

pfgsea(rankedList, gmtFiles, nPerm = 1000L, minSize = 15L,
  maxSize = 500L, alpha = 0.05, BPPARAM = BiocParallel::bpparam())

Arguments

rankedList

RankedList. Ranked gene list.

gmtFiles

character. GMT file paths.

nPerm

integer(1). Number of permutations. Minimial possible nominal P value is about 1/nPerm.

minSize

integer(1). Minimal size of a gene set to test. All pathways below the threshold are excluded.

maxSize

integer(1)/Inf. Maximal size of a gene set to test. All pathways above the threshold are excluded.

alpha

numeric(1). Alpha level cutoff. Stored internally in metadata(). Applied only to plots and enriched gene set exports, but does not affect the actual GSEA enrichment calculation.

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

Value

FGSEAList.

Note

Updated 2019-10-11.

Examples

data(gsea) metadata <- S4Vectors::metadata rankedList <- metadata(gsea)[["rankedList"]] gmtFiles <- metadata(gsea)[["gmtFiles"]] # Copy example MSigDb files to `$HOME`. file.copy( from = system.file( "extdata", "msigdb", package = "pfgsea", mustWork = TRUE ), to = "~", overwrite = FALSE, recursive = TRUE )
#> [1] FALSE
x <- pfgsea(rankedList = rankedList, gmtFiles = gmtFiles)
#> Running parameterized fast GSEA... #> GMT files: h #> Contrasts: dmso_r1881_vs_etoh
#> GMT file: h.all.v6.2.symbols.gmt #> Testing against 50 pathways. #> Running using 1000 permutations.
#> FGSEAList 0.1.14 of length 1 #> collectionNames: h #> contrastNames: dmso_r1881_vs_etoh