browseGenome

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Browse a genome

A generic function for launching a genome browser.

Keywords
interface
Usage
browseGenome(object, ...) "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.

See Also

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

Aliases
  • browseGenome
  • GenomicRangesORGenomicRangesList-class
  • browseGenome,GenomicRangesORGenomicRangesList-method
  • browseGenome,missing-method
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)
Documentation reproduced from package rtracklayer, version 1.32.1, License: Artistic-2.0 + file LICENSE

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