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), view = TRUE,
             trackParams = list(), viewParams = list(), ...)

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.
view Whether to open a view.
trackParams
viewParams
... 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 1.2.2 Index]