argoSession-class {rtracklayer}R Documentation

Class "argoSession"

Description

An object representing a session in the Argo genome browser.

Objects from the Class

Objects may be created by calls of the form browserSession("argo", name, jar) where name is the name of the session in Argo and jar is the path to the installed Argo jar file.

Slots

jref:
Object of class "jobjRef" holding the reference to the low-level Argo object.
seqcache:
Object of class "environment" that caches sequence objects after lookup from UCSC.

Extends

Class "browserSession", directly.

Methods

activeView(object)
Obtains the currently active browserView for this session.
activeView<-(object)
Sets the currently active view for this session.
browserView(object, segment = genomeSegment(object),track = tracks(object, segment, TRUE), ...)
Creates a browserView of segment with visible tracks named in track. Parameters in ... correspond to slots in the genomeSegment class and override those in segment.
browserViews(object)
Gets a list of the browserView instances for this session.
close(con)
Closes this session.
genomeSequence(object, segment)
Gets the genome sequence in segment.
laySequence(object, sequence, name, label = name)
Stores sequence under name, labeled as label in the user interface.
layTrack(object, track, name = deparse(substitute(track)), view = TRUE)
Stores track under name, opening a view of the track if view is TRUE.
trackSet(object, name, segment = genomeSegment(object))
Obtains a trackSet named name from segment.
tracks(object, segment = NULL, visible = FALSE)
Gets the names of tracks in segment. If visible is TRUE, only the visible tracks are returned. Note that in Argo tracks are visible on a global, not per-session nor per-view, basis.

Note

In order to use this backend, the Argo jar file must be manually downloaded from the URL in the references. The call to browserSession must then pass the path to the jar file as the jar parameter. By default, the path is the ‘java’ directory of the rtracklayer package.

Author(s)

Michael Lawrence

References

The Argo genome browser: http://www.broad.mit.edu/annotation/argo/

See Also

browserSession for creating instances of this class.


[Package rtracklayer version 1.2.2 Index]