browseGenome {rtracklayer}R Documentation

Browse a genome

Description

A generic function for launching a genome browser.

Usage

browseGenome(object, ...)
## S4 method for signature 'RangedDataORRangedDataList':
browseGenome(object = RangedDataList(),
  browser = "ucsc", range = range(tracks),
  view = TRUE, trackParams = list(), viewParams = list(), ...)

Arguments

object A list of RangedData instances, e.g. a RangedDataList instance.
browser The name of the genome browser.
range The 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.
... Arguments corresponding to slots in RangesList that override those in range.

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 <- GenomicRanges("hg18", "chr22", 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(RangedDataList(track))
  
## End(Not run)

[Package rtracklayer version 1.4.1 Index]