performGOenrichment.diffMeth.entrez {RnBeads}R Documentation

performGOenrichment.diffMeth.entrez

Description

performs Gene Ontology (GO) enrichment analysis for a list of Entrez identifiers

Usage

performGOenrichment.diffMeth.entrez(gids, uids, ontology, assembly = "hg19",
  ...)

Arguments

gids

gene ids to test (entrez IDs)

uids

ids to test against (universe)

ontology

which ontology should be used (see GOHyperGParams from the GOstats package for details)

assembly

Genome to be used. One of the following: hg19, mm9, mm10 or rn5

...

arguments passed on to the parameters of GOHyperGParams from the GOstats package

Value

a GOHyperGresult object (see the GOstats package for further details)

Author(s)

Fabian Mueller

Examples


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")
[Package RnBeads version 1.10.8 Index]