HTSanalyzeR (version 2.24.0)

multiHyperGeoTest: Hypergeometric tests on a list of gene sets

Description

This function performs hypergeometric tests for over-representation of hits, on a list of gene sets. This function applies the function hyperGeoTest to an entire list of gene sets and returns a data frame.

Usage

multiHyperGeoTest(collectionOfGeneSets, universe, hits, minGeneSetSize =
15, pAdjustMethod = "BH", verbose = TRUE)

Arguments

collectionOfGeneSets

a list of gene sets, each of which is a character vector of gene identifiers

universe

a character vector of all gene identifiers (usually all genes tested in a screen)

hits

a character vector of gene identifiers for those considered as hits

minGeneSetSize

a single integer or numeric value specifying the minimum number of elements in a gene set that must map to elements of the gene universe. Gene sets with fewer genes than this number are removed from both hypergeometric analysis and GSEA.

pAdjustMethod

a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details)

verbose

a single logical value indicating to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

Value

a data frame containing the results of the hypergeometric test (one row per gene set)

See Also

hyperGeoTest

Examples

##example 1
gl <- runif(100, min=0, max=5)
gl <- gl[order(gl, decreasing=TRUE)]
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<-multiHyperGeoTest(collectionOfGeneSets=gsc, universe=names(gl), 
hits=names(gl)[which(abs(gl) > 2)], minGeneSetSize = 2, pAdjustMethod ="BH")
##example 2
## Not run: 
# 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")
# DM_KEGG <- KeggGeneSets(species="Dm")
# ##Do multiple hypergeometric tests
# hypgeoResults <- multiHyperGeoTest(collectionOfGeneSets=DM_KEGG,
# universe=names(KcViab_Data4Enrich), hits=names(KcViab_Data4Enrich)[which(abs(
# KcViab_Data4Enrich) > 2)], minGeneSetSize = 15, pAdjustMethod = "BH")
# ## End(Not run)