browseGenome: Browse a genome

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

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 IntegerRangesList 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)

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.