performGoEnrichment.diffMeth {RnBeads} | R Documentation

## performGoEnrichment.diffMeth

### Description

performs Geno Ontology (GO) enrichment analysis for a given differential methylation table.

### Usage

    performGoEnrichment.diffMeth(rnbSet, diffmeth, ontologies = c("BP", "MF"),
      rank.cuts.region = c(100, 500, 1000), add.auto.rank.cut = TRUE,
      rerank = TRUE, verbose = TRUE, ...)

### Arguments

`rnbSet` | RnBSet object for which dirrential methylation was computed
`diffmeth` | RnBDiffMeth object. See `RnBDiffMeth-class` for details.
`ontologies` | GO ontologies to use for enrichment analysis
`rank.cuts.region` | Cutoffs for combined ranking that are used to determine differentially methylated regions
`add.auto.rank.cut` | flag indicating whether an automatically computed cut-off should also be considered.
`rerank` | For deterimining differential methylation: should the ranks be ranked again or should the absolute ranks be used.
`verbose` | Enable for detailed status report
`...` | arguments passed on to the parameters of `GOHyperGParams` from the `GOstats` package

### Value

a DiffMeth.go.enrich object (S3) containing the following attributes

`region` | Enrichment information for differential methylation on the region level. See `GOHyperGresult` from the `GOstats` package for furthert 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"))
    res <- performGoEnrichment.diffMeth(rnb.set.example,dm)

[Package RnBeads version 1.12.1 Index]