performGOenrichment.diffMeth.entrez {RnBeads} | R Documentation |
performs Gene Ontology (GO) enrichment analysis for a list of Entrez identifiers
performGOenrichment.diffMeth.entrez( gids, uids, ontology, assembly = "hg19", ... )
gids |
gene ids to test (entrez IDs) |
uids |
ids to test against (universe) |
ontology |
which ontology should be used (see |
assembly |
Genome to be used. One of the following: hg19, mm9, mm10 or rn5 |
... |
arguments passed on to the parameters of |
a GOHyperGresult
object (see the GOstats
package for further details)
Fabian Mueller
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment")) dmt <- get.table(dm,get.comparisons(dm)[1],"promoters") annot <- annotation(rnb.set.example,"promoters") all.promoters <- annot$entrezID #get the hypermethylated promoters hyper.promoters <- annot$entrezID[dmt[,"mean.mean.diff"]>0] result <- performGOenrichment.diffMeth.entrez(hyper.promoters,all.promoters,"BP",assembly="hg19")