performLolaEnrichment.diffMeth: performLolaEnrichment.diffMeth

In RnBeads: RnBeads

Description

performs LOLA enrichment analysis for a given differential methylation table.

Usage

performLolaEnrichment.diffMeth(
  rnbSet,
  diffmeth,
  lolaDbPaths,
  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.
lolaDbPaths	LOLA database paths
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

Value

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

region	Enrichment information for differential methylation on the region level. A data.table object as returned by the runLOLA function from the LOLA package for furthert details. Each element will contain different user sets for different rank cutoffs and hyper/hypomethylation events(userSet column)
lolaDb	The loaded lolaDb object containing the merged databases as returned by loadLolaDbs

Author(s)

Fabian Mueller

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
# compute differential methylation
dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
# download LOLA DB
lolaDest <- tempfile()
dir.create(lolaDest)
lolaDirs <- downloadLolaDbs(lolaDest, dbs="LOLACore")
# perform enrichment analysis
res <- performLolaEnrichment.diffMeth(rnb.set.example,dm,lolaDirs[["hg19"]])

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