RunFgseaOnRankList: RunFgseaOnRankList - wrapper around fast gene set enrichment...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

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

Description

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

Examples

# usage:
t1hvl_rank = GetRankResultsRaw(limma.fit.object.list  = ebf, coefficient.number = 1, contrast.name = "time_1_highvslow")
gsea = RunFgseaOnRankList(rank.list.celltype = t1hvl_rank, )

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.