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 1.12.1 Index]