performGoEnrichment.diffMeth {RnBeads} | R Documentation |
performs Geno Ontology (GO) enrichment analysis for a given differential methylation table.
performGoEnrichment.diffMeth( rnbSet, diffmeth, ontologies = c("BP", "MF"), rank.cuts.region = c(100, 500, 1000), add.auto.rank.cut = TRUE, rerank = TRUE, verbose = TRUE, ... )
rnbSet |
RnBSet object for which dirrential methylation was computed |
diffmeth |
RnBDiffMeth object. See |
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 |
a DiffMeth.go.enrich object (S3) containing the following attributes
region |
Enrichment information for differential methylation on the region level. See |
Fabian Mueller
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)