browserSession-class {rtracklayer}R Documentation

Class "browserSession"

Description

An object representing a genome browser session. Each session corresponds to a set of loaded trackSet instances and a set of browserView instances. Note that this is a virtual class; a concrete implementation is provided by each backend driver.

Objects from the Class

A virtual Class: No objects may be created from it. See browserSession for obtaining an instance of an implementation for a particular genome browser.

Methods

This specifies the API implemented by each browser backend. Note that a backend is not guaranteed to support all operations.

browserView(object, segment = genomeSegment(object), track = tracks(object), ...)
Constructs a browserView of segment for this session.
browserViews(object, ...)
Gets the browserView instances belonging to this session.
activeView(object, ...)
Returns the browserView that is currently active in the session.
genomeSegment(object, ...)
Gets the genomeSegment representing the segment of the genome currently displayed by the browser (i.e. the segment shown by the active view) or a default value (possibly NULL) if no views exist.
genomeSequence(object, segment = genomeSegment(object), ...)
gets a genomic sequence of segment from this session.
laySequence(object, ...)
Loads a sequence into the session.
layTrack(object, track, name = deparse(substitute(track)), view = TRUE, ...)
Loads one or more tracks into the session and optionally open a view of the track.
trackSet(object, segment = genomeSegment(object), name, ...)
Gets features in segment in the track stored as name as a trackSet.
tracks(object, ...)
Gets the names of the tracks stored in this session.
close(con, ...)
Close this session.
show(object, ...)
Output a textual description of this session.

Author(s)

Michael Lawrence

See Also

browserSession for obtaining implementations of this class for a particular genome browser.


[Package rtracklayer version 1.2.2 Index]