fgseaCelliD {CelliD}R Documentation

Slight change in fgsea for ram and speed efficiency in CelliD

Description

Slight change in fgsea for ram and speed efficiency in CelliD

Usage

fgseaCelliD(
  pathways,
  stats,
  nperm = 1000,
  minSize = 10,
  maxSize = 500,
  gseaParam = 0
)

Arguments

pathways

List of gene sets to check

stats

Named vector of gene-level stats. Names should be the same as in 'pathways'

nperm

Number of permutations to do. Minimal possible nominal p-value is about 1/nperm

minSize

Minimal size of a gene set to test. All pathways below the threshold are excluded.

maxSize

Maximal size of a gene set to test. All pathways above the threshold are excluded.

gseaParam

GSEA parameter value, all gene-level stats are raised to the power of 'gseaParam' before calculation of GSEA enrichment scores

Value

A table with GSEA results. Each row corresponds to a tested pathway. The columns are the following:

Examples

seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
ranking <- GetCellGeneRanking(seuratPbmc, reduction = "mca", dims = 1:5)
fgseaCelliD(pathways = Hallmark, stats = ranking[[1]])

[Package CelliD version 1.0.0 Index]