rnb.RnBSet.to.bed: rnb.RnBSet.to.bed

Description

convert an RnBSet object to *.bed files.

Usage

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

Arguments

rnb.set

Object of class 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 converted

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

verbose

More detailed logger output

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).

Details

Details on bed 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].

Examples

Run this code


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