RnBeads (version 1.4.0)

rnb.export.to.trackhub: rnb.export.to.trackhub

Description

convert an RnBSet object to a UCSC-style track hub.

Usage

rnb.export.to.trackhub(rnb.set, out.dir, reg.type = "sites", data.type = "bigBed", ...)

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

data.type

either "bigBed" or "bigWig"

...

parameters passed on to the track hub generating procedure

Value

a list containing information on the export

Details

During execution the RnBSet is converted to bed files. If the operating system is supported (currently Unix and MacOS only) these are automatically converted to bigBed files. If your operating system is not supported, you need to create them manually (see the UCSC Genome Browser documentation for details). For details on UCSC track hubs see the UCSC tracks help page.

Examples

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