rnb.RnBSet.to.bed: Export to BED files

In RnBeads: RnBeads

Description

Exports the beta values from a methylation dataset to BED files.

Usage

rnb.RnBSet.to.bed(
  rnb.set,
  out.dir,
  reg.type = "sites",
  names.quant.meth = TRUE,
  add.track.line = TRUE,
  lexicographic = FALSE,
  verbose = TRUE
)

Arguments

rnb.set	Methylation dataset as an object of type inheriting RnBSet.
out.dir	Output directory. If not existing, it will be created. otherwise files in that directory are overwritten.
reg.type	Region type to be extracted.
names.quant.meth	should the names of the bed regions contain information on the methylation level. If TRUE the following format is applied: meth_percent covg(rnb.set) is not NULL
add.track.line	Add a track line to the bed file to enable browsers like IGV to display the data better
lexicographic	Should lexicographic ordering be used for chromosome names
verbose	More detailed logger output

Details

Details on the BED file format can be found in the UCSC Genome Browser documentation. Each methylation site is an entry in the resulting bed file. The Score column corresponds to a site's methylation value in the interval [0,1].

Value

(invisibly) a summary list containing information on the conversion step. elements are filenames (a table containing information on which sample has been written to what filename) and assembly (a string indicating the assembly used by rnb.set).

Author(s)

Fabian Mueller

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
rnb.RnBSet.to.bed(rnb.set.example,tempdir())

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