gsFisherTestCore: The core algorithm to perform Fisher's exact test on a gene...

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

The core algorithm to perform Fisher's exact test on a gene set

Description

The core algorithm to perform Fisher's exact test on a gene set

Usage

gsFisherTestCore(
  genes,
  geneSetGenes,
  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
geneSetGenes	Character vector, genes belonging to a 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 three elements

1. p The p-value of one-sided (over-representation of the Fisher's test)

2. gsEffectiveSize Gene-set's effective size, namely number of genes that are in the universe

3. 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
gsFisherTestCore(myGenes, myGeneSet1, myUniverse)
gsFisherTestCore(myGenes, myGeneSet2, myUniverse)

## use EASE for conservative estimating
gsFisherTestCore(myGenes, myGeneSet1, myUniverse, useEASE=FALSE)
gsFisherTestCore(myGenes, myGeneSet1, myUniverse, useEASE=TRUE)

## checkUniverse will make sure that \code{univese} contains all element in \code{genes}
gsFisherTestCore(c("OutOfUniverse", myGenes), myGeneSet1, myUniverse, checkUniverse=FALSE)
gsFisherTestCore(c("OutOfUniverse", myGenes), myGeneSet1, myUniverse, checkUniverse=TRUE)

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