exportDMRs2regionFile: exportDMRs2regionFile

In RnBeads: RnBeads

Description

export differentially methylated regions to region file (standard bed). The output is in BED6 format where the score corresponds to to the combined rank (rank==1 would receive a score of 1000 and a combined rank equal to the number of regions a score of 0)

Usage

exportDMRs2regionFile(
  rnbSet,
  diffmeth,
  dest,
  comp.name,
  region.type,
  rank.cut = NULL,
  rerank = FALSE
)

Arguments

rnbSet	the RnBSet object for which the DMRs were computed.
diffmeth	DiffMeth object. See rnb.execute.computeDiffMeth for details.
dest	destination file name
comp.name	name of the comparison
region.type	region type.
rank.cut	rank cutoff. If NULL (default), all regions are processed.
rerank	flag indicating whether the ranks should be reranked or whether rank.cut refers to the absolute rank

Value

NULL

Author(s)

Fabian Mueller

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
dm <- rnb.execute.computeDiffMeth(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
exportDMRs2regionFile(rnb.set.example,dm,tempfile(),get.comparisons(dm)[1],"promoters")

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