browseGenome {rtracklayer}R Documentation

Browse a genome

Description

A generic function for launching a genome browser.

Usage

browseGenome(object, ...)
## S4 method for signature 'GenomicRanges_OR_GenomicRangesList'
browseGenome(object,
  browser = "UCSC", range = base::range(object),
  view = TRUE, trackParams = list(), viewParams = list(),
  name = "customTrack", ...)

Arguments

object

A GRanges object or a list of GRanges objects (e.g. a GenomicRangesList object).

browser

The name of the genome browser.

range

A genome identifier or a GRanges or RangesList to display in the initial view.

view

Whether to open a view.

trackParams

Named list of parameters to pass to track<-.

viewParams

Named list of parameters to pass to browserView.

name

The name for the track.

...

Arguments passed to browserSession.

Value

Returns a BrowserSession.

Author(s)

Michael Lawrence

See Also

BrowserSession and BrowserView, the two main classes for interfacing with genome browsers.

Examples

  ## Not run: 
  ## open UCSC genome browser:
  browseGenome()
  ## to view a specific range:
  range <- GRangesForUCSCGenome("hg18", "chr22", IRanges(20000, 50000))
  browseGenome(range = range)
  ## a slightly larger range:
  browseGenome(range = range, end = 75000)
  ## with a track:
  track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
  browseGenome(GRangesList(track))
  
## End(Not run)
[Package rtracklayer version 1.38.3 Index]