collapsePathways: Collapse list of enriched pathways to independent ones.

In ctlab/fgsea: Fast Gene Set Enrichment Analysis

Collapse list of enriched pathways to independent ones.

Description

Collapse list of enriched pathways to independent ones.

Usage

collapsePathways(
  fgseaRes,
  pathways,
  stats,
  pval.threshold = 0.05,
  nperm = 10/pval.threshold,
  gseaParam = 1
)

Arguments

fgseaRes	Table with results of running fgsea(), should be filtered by p-value, for example by selecting ones with padj < 0.01.
pathways	List of pathways, should contain all the pathways present in 'fgseaRes'.
stats	Gene-level statistic values used for ranking, the same as in 'fgsea()'.
pval.threshold	Two pathways are considered dependent when p-value of enrichment of one pathways on background of another is greater then 'pval.threshold'.
nperm	Number of permutations to test for independence, should be several times greater than '1/pval.threhold'. Default value: '10/pval.threshold'.
gseaParam	GSEA parameter, same as for 'fgsea()'

Value

Named list with two elments: 'mainPathways' containing IDs of pathways not reducable to each other, and 'parentPathways' with vector describing for all the pathways to which ones they can be reduced. For pathways from 'mainPathwyas' vector 'parentPathways' contains 'NA' values.

Examples

data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=10000, maxSize=500)
collapsedPathways <- collapsePathways(fgseaRes[order(pval)][padj < 0.01],
                                      examplePathways, exampleRanks)
mainPathways <- fgseaRes[pathway %in% collapsedPathways$mainPathways][
                         order(-NES), pathway]

ctlab/fgsea documentation built on Oct. 28, 2023, 7:09 p.m.