gsListFisherTestCore: Core algorithm to perform Fisher's exact test on a list of...
In bedapub/ribiosGSEA: Gene-Set Enrichment Analysis Tools in Ribios

gsListFisherTestCore

R Documentation

Core algorithm to perform Fisher's exact test on a list of gene set

Description

Core algorithm to perform Fisher's exact test on a list of gene set

Usage

gsListFisherTestCore(
  genes,
  geneSetGenesList,
  universe,
  makeUniqueNonNA = TRUE,
  checkUniverse = TRUE,
  useEASE = FALSE
)

Arguments

`genes`	Character vector, a collection of genes of which over-representation of the gene set is tested
`geneSetGenesList`	A list of character vector, genes belonging to each gene set
`universe`	Character vector, universe of genes
`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 the genes given as `geneSetGenes` in the input `genes` 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.

Value

A list of lists, of the same length as the input geneSetGenesList, each list consisting of three elements

p The p-value of one-sided (over-representation of the Fisher's test)
gsEffectiveSize Gene-set's effective size, namely number of genes that are in the universe
hits Character vector, genes that are found in the gene sets

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
gsListFisherTestCore(myGenes, list(myGeneSet1, myGeneSet2), myUniverse)

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