RunFgseaOnRankList - wrapper around fast gene set enrichment analysis with the fgsea R package https://bioconductor.org/packages/release/bioc/html/fgsea.html

RunFgseaOnRankList - wrapper around fast gene set enrichment analysis with the fgsea R package https://bioconductor.org/packages/release/bioc/html/fgsea.html

Usage

RunFgseaOnRankList(
  ...,
  rank.list.celltype,
  pathways,
  maxSize = 500,
  minSize = 9,
  nperm = 250000,
  positive.enrich.only = FALSE
)

Arguments

rank.list.celltype

results returned by GetRankResultsRaw or GetRankResults

pathways

modules / gene sets as a named list each a single vector of unique gene IDS

maxSize

see fgsea package

minSize

see fgsea package

nperm

recommended to keep set at 25000 based on optomization and p value stabilization

positive.enrich.only

include negative enrichments in results? TRUE/FALSE

Value

Examples

# usage:
t1hvl_rank = GetRankResultsRaw(limma.fit.object.list  = ebf, coefficient.number = 1, contrast.name = "time_1_highvslow")
#> Error in GetRankResultsRaw(limma.fit.object.list = ebf, coefficient.number = 1,     contrast.name = "time_1_highvslow"): unused arguments (limma.fit.object.list = ebf, coefficient.number = 1, contrast.name = "time_1_highvslow")
gsea = RunFgseaOnRankList(rank.list.celltype = t1hvl_rank, )
#> Warning: 'RunFgseaOnRankList' is deprecated.
#> Use 'FgseaList' instead.
#> See help("Deprecated")
#> Error in RunFgseaOnRankList(rank.list.celltype = t1hvl_rank, ): object 't1hvl_rank' not found