R: performGOEnrichment.diffVar

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 2.5.0 Index]