fisherTest-character-list-character-method: Perform Fisher's exact test on a GeneSet object

fisherTest,character,list,character-methodR Documentation

Perform Fisher's exact test on a GeneSet object

Description

Perform Fisher's exact test on a GeneSet object

Usage

## S4 method for signature 'character,list,character'
fisherTest(
  genes,
  genesets,
  universe,
  makeUniqueNonNA = TRUE,
  checkUniverse = TRUE,
  useEASE = FALSE
)

Arguments

genes

a collection of genes of which over-representation of the gene set is tested

genesets

A GmtList object.

universe

universe of genes

makeUniqueNonNA

Logical, whether genes and universe should be filtered to remove NA and made unique. The default is set to TRUE. When the uniqueness and absence of NA is ensured, this flag can be set to FALSE to accelerate the operation.

checkUniverse

Logical, if TRUE, then genes that are in genes but are not in universe are appended to universe

useEASE

Logical, whether to use the EASE method to report the p-value.

This function performs one-sided Fisher's exact test to test the over-representation of gene set genes in the input gene list.

Examples

myGenes <- LETTERS[1:3]
myS4GeneSet1 <- list(name="GeneSet1", desc="GeneSet", 
    genes=LETTERS[1:6], namespace="My namespace 1")
myS4GeneSet2 <- list(name="GeneSet1", desc="GeneSet", 
    genes=LETTERS[2:7], namespace="My namespace 2")
myUniverse <- LETTERS
fisherTest(myGenes, myS4GeneSet1, myUniverse)
fisherTest(myGenes, myS4GeneSet2, myUniverse)

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