RnBeads (version 1.4.0)

exportDMRs2regionFile: 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

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")