fisherTestEdgeResult: Run Fisher's exact test on an EdgeResult object

In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

Run Fisher's exact test on an EdgeResult object

Description

Run Fisher's exact test on an EdgeResult object

Usage

fisherTestEdgeResult(
  edgeResult,
  gmtList,
  contrast,
  thr.abs.logFC = 1,
  thr.FDR = 0.05,
  minGeneSetEffectiveSize = 5,
  maxGeneSetEffectiveSize = 500,
  ...
)

Arguments

edgeResult	An EdgeResult object
gmtList	A GmtList or GeneSets object
contrast	Character, the contrast of interest
thr.abs.logFC	Numeric, threshold of absolute log2 fold-change to define positively and negatively regulated genes
thr.FDR	Numeric, threshold of FDR values
minGeneSetEffectiveSize	Integer, minimal number of genes of a geneset that are quantified
maxGeneSetEffectiveSize	Integer, maximal number of genes of a geneset that are quantified
...	Passed to filter to further filter the differential gene expression table (dgeTbl).

Value

## TODO: example

bedapub/ribiosGSEA documentation built on March 30, 2023, 3:26 p.m.