fisherTest-character-character-character-method: Perform Fisher's exact test on a gene set
In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

fisherTest,character,character,character-method

R Documentation

Perform Fisher's exact test on a gene set

Description

Perform Fisher's exact test on a gene set

Usage

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

Arguments

`genes`	a collection of genes of which over-representation of the gene set is tested
`genesets`	A vector of character strings, genes belonging to one gene set.
`universe`	universe of genes
`gsName`	gene set name, can be left missing
`gsNamespace`	gene set namespace name, can be left missing
`makeUniqueNonNA`	Logical, whether genes, geneSetGenes, 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. If `useEASE` is `TRUE`, one gene is penalized (removed) within `geneSetGenes` that are in `genes` and calculating the resulting Fisher exact probability for that namespace. The theoretical basis of the EASE score lies in the concept of jackknifing a probability. See Hosack et al. for details.

Note

Duplicated items in genes, genesets' genes, and the universe are per default removed

References

Hosack et al.: Hosack, Douglas A., Glynn Dennis, Brad T. Sherman, H. Clifford Lane, and Richard A. Lempicki. Identifying Biological Themes within Lists of Genes with EASE. Genome Biology 4 (2003): R70. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/gb-2003-4-10-r70")}

Examples

myGenes <- LETTERS[1:3]
myGeneSet1 <- LETTERS[1:6]
myGeneSet2 <- LETTERS[4:7]
myUniverse <- LETTERS
fisherTest(genes=myGenes, genesets=myGeneSet1, universe=myUniverse)
fisherTest(genes=myGenes, genesets=myGeneSet2, universe=myUniverse)
fisherTest(genes=myGenes, genesets=myGeneSet1, universe=myUniverse, 
           gsName="My gene set1", gsNamespace="Letters")

## note that duplicated items are removed by default
resWoRp <- fisherTest(genes=rep(myGenes,2), genesets=myGeneSet1, 
                      universe=myUniverse)
resWithRp <- fisherTest(genes=rep(myGenes,2), genesets=myGeneSet1, 
                      universe=rep(myUniverse,2))
identical(resWoRp, resWithRp)

resWithRpNoUnique <- fisherTest(genes=rep(myGenes,2), genesets=myGeneSet1, 
           universe=rep(myUniverse,2), makeUniqueNonNA=FALSE)
identical(resWoRp, resWithRpNoUnique)

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