R: exportDMRs2regionFile

exportDMRs2regionFile {RnBeads}

R Documentation

exportDMRs2regionFile

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")

[Package RnBeads version 2.5.0 Index]