multiHyperGeoTest {HTSanalyzeR} | R Documentation |
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.
multiHyperGeoTest(collectionOfGeneSets, universe, hits, minGeneSetSize = 15, pAdjustMethod = "BH", verbose = TRUE)
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) |
a data frame containing the results of the hypergeometric test (one row per gene set)
John C. Rose, Xin Wang
##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)