browseGenome {rtracklayer}R Documentation

Browse a genome

Description

A generic function for launching a genome browser.

Usage

browseGenome(tracks = trackSets(), browser = "ucsc", segment = genomeSegment(tracks), ...)

Arguments

tracks A list of trackSet instances, e.g. a trackSets instance.
browser The name of the genome browser.
segment The genomeSegment to display in the initial view.
... Arguments corresponding to slots in genomeSegment that override those in segment.

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 segment:
  segment <- genomeSegment("hg18", "chr22", 20000, 50000)
  browseGenome(segment = segment)
  ## a slightly larger segment:
  browseGenome(segment = segment, end = 75000)
  ## with a track:
  track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
  browseGenome(trackSets(track))
  
## End(Not run)

[Package rtracklayer version 1.0.0 Index]