fgseaCellID: reworked fgsea for ram and speed efficiency in CellID

Description Usage Arguments Value Examples

View source: R/gsea.R

Description

reworked fgsea for ram and speed efficiency in CellID

Usage

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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. Minimial 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 statis 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

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data(examplePathways)
data(exampleRanks)
fgseaRes <- fgsea(Hallmark, exampleRanks, nperm = 1000, maxSize = 500)

cbl-imagine/cellID documentation built on Nov. 12, 2019, 1:36 a.m.