performGOEnrichment.diffVar {RnBeads} | R Documentation

## performGOEnrichment.diffVar

### Description

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

### Usage

    performGOEnrichment.diffVar(
      rnbSet,
      diffmeth,
      enrich.diffMeth = NULL,
      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 variability was computed
`diffmeth` | RnBDiffMeth object. See `RnBDiffMeth-class` for details.
`enrich.diffMeth` | Result of `performGOEnrichment.diffMeth`. NULL, if enrichment should only be performed for differential variability.
`ontologies` | GO ontologies to use for enrichment analysis
`rank.cuts.region` | Cutoffs for combined ranking that are used to determine differentially variable regions
`add.auto.rank.cut` | flag indicating whether an automatically computed cut-off should also be considered.
`rerank` | For deterimining differential variability: 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.enrich object (S3) containing the following attributes

`region` | Enrichment information for differential variability on the region level. See `GOHyperGresult` from the `GOstats` package for furthert details

### Author(s)

Fabian Mueller and Michael Scherer

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    dm <- rnb.execute.diffVar(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
    res <- performEnrichment.diffVar(rnb.set.example,dm)

[Package RnBeads version 2.12.2 Index]