collapsePathways: Collapse list of enriched pathways to independent ones.
In fgsea: Fast Gene Set Enrichment Analysis

Description Usage Arguments Value Examples

Collapse list of enriched pathways to independent ones.

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

`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()'

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.

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]

sh: 1: wc: Permission denied
Warning message:
In fgsea(examplePathways, exampleRanks, nperm = 10000, maxSize = 500) :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.