igbTrack-class: Class '"igbTrack"'

Description Objects from the Class Slots Methods Author(s) References See Also Examples

Description

This class represents a single "track" within IGB's display portion. Slots indicate all information IGB requires to add the track to the current display.

Objects from the Class

Objects can be created by calls of the form new("igbTrack", ...).

Slots

genome:

A character value indicating the genome in question. Must be of the form used by IGB, eg H_apiens_Feb_2009

loadmode:

Character value indicating how the data should be loaded. Must be one of "REGION_IN_VIEW", "WHOLE_CHROMOSOME", and "WHOLE_GENOME"

refresh:

Logical indicating whether the view should be refreshed after loading the data. Defaults to TRUE.

uri:

A character value containing the full path or URL to the file containing data for the track.

Methods

genome<-

Sets the genome value for the track.

genome

Returns the current value genome of the track.

loadmode<-

Sets the loadmode value for the track.

loadmode

Returns the current loadmode for the slot.

refresh<-

Sets the refresh value for the track.

refresh

Returns the current refresh value for the track.

track<-

Displays the indicated igbTrack in the igbSession

uri<-

Sets the URI of the data to be displayed by the track.

uri

Returns the URI for the data displayed by the track.

ViewInIGB

Show track in running IGB session

Author(s)

Gabriel Becker

References

Vora, Hiral. "Scripting", IGB User's Guide, bioviz, Nov 1, 2011. http://wiki.transvar.org/confluence/display/igbman/Scripting

See Also

igbSession

Examples

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hsaptrk =igbTrack(genome = "H_sapiens_Feb_2009",
  uri="http://netaffxdas.affymetrix.com/quickload_data/H_sapiens_Feb_2009/cytoBand.cyt",
  loadmode="REGION_IN_VIEW", refresh=TRUE
  )

gmbecker/rigbLite documentation built on May 14, 2017, 12:57 p.m.