performGOenrichment.diffMeth.entrez: performGOenrichment.diffMeth.entrez

In RnBeads: RnBeads

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")

RnBeads documentation built on March 3, 2021, 2 a.m.