LeadingEdgeIndexed - extract leading edge genes from FgseaList results, return a new embedded list of named modules, indexed by celltype

LeadingEdgeIndexed - extract leading edge genes from FgseaList results, return a new embedded list of named modules, indexed by celltype

Usage

LeadingEdgeIndexed(gsea.result.list, padj.threshold = 0.05, p.threshold = NULL)

Arguments

gsea.result.list

results from FgseaList or RunFgseaOnRankList

padj.threshold

within each cell type return list of leading edge genes with padj less than this parameter value.

Value

embedded list - each list level 1 indexed by cell type, contains a new list level 2, the leading edge genes from the gsea results filtered by padj.

Examples

if (FALSE) {
t1hvl_rank = GetRankResultsRaw(limma.fit.object.list  = ebf,
coefficient.number = 1,
contrast.name = "time_1_highvslow")
gsea = FgseaList(rank.list.celltype = t1hvl_rank)
celltype.indexed.modules.leadingedge = LeadingEdgeIndexed(gsea, 0.05)
}