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 2.12.2 Index]