hyperGeoTest: Performs hypergeometric tests for over-representation...

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This function takes in a single gene set (geneSet), a vector of gene identifiers for all tested genes (universe), a vector of "hits" (hits), and a p-value adjustment method. It outputs a vector containing the size of the gene universe, the size of the gene set within this universe (i.e. how many genes from the universe map to this gene set), the total number of hits, the number of hits expected to occur in the gene set, the actual hits observed in the gene set, and the p-value from a hypergeometric test.

Usage

hyperGeoTest(geneSet, universe, hits)

Arguments

geneSet	a character vector specifying a gene set
universe	a character vector of all gene identifiers (usually all genes tested in a screen)
hits	a character vector of gene identifiers for those genes considered as hits

Value

a numeric vector containing the size of the gene universe (named by "Universe Size"), the size of the gene set within this universe (i.e. how many genes from the universe map to this gene set (named by "Gene Set Size"), the total number of hits (named by "Total Hits"), the number of hits expected to occur in the gene set (named by "Expected Hits"), the actual hits observed in the gene set (named by "Observed Hits"), and the pvalue from a hypergeometric test (named by "Pvalue").

Author(s)

John C. Rose, Xin Wang

See Also

multiHyperGeoTest

Examples

##example 1
gl <- runif(100, min=0, max=5)
gl <- order(gl)
names(gl) <- as.character(sample(x=seq(from=1, to=100, by=1), size=100,
replace=FALSE))
gs1 <- sample(names(gl), size=20, replace=FALSE)
gs2 <- sample(names(gl), size=20, replace=FALSE)
gsc <- list(subset1=gs1, subset2=gs2)
hypgeo <- hyperGeoTest(geneSet=gsc[["subset1"]], universe=names(gl), 
hits=names(gl)[which(abs(gl) > 2)])
##example 2 
library(org.Dm.eg.db)
library(KEGG.db)
##load phenotype vector (see the vignette for details about the
##preprocessing of this data set)
data("KcViab_Data4Enrich")
##Prepare kegg gene sets
DM_KEGG<-KeggGeneSets(species="Dm")
##Do the tests
hypgeoResults <- hyperGeoTest(geneSet=DM_KEGG[[1]], universe=
names(KcViab_Data4Enrich), hits=names(KcViab_Data4Enrich)[which(abs(
KcViab_Data4Enrich) > 2)])

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.