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

In RnBeads: RnBeads

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

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.

Value

a list containing information on the export

Author(s)

Fabian Mueller

Examples

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

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