performGOEnrichment.diffVar: performGOEnrichment.diffVar

In RnBeads: RnBeads

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)

RnBeads documentation built on March 3, 2021, 2 a.m.