ucscSession-class {rtracklayer}R Documentation

Class "ucscSession"

Description

An implementation of browserSession for the UCSC genome browser.

Objects from the Class

Objects can be created by calls of the form browserSession("ucsc", url = "http://genome.ucsc.edu/cgi-bin").

Slots

url:
Object of class "character" holding the base URL of the UCSC browser.
hguid:
Object of class "numeric" holding the user identification code.
views:
Object of class "environment" containing a list stored under the name "instances". The list holds the instances of browserView for this session.

Extends

Class "browserSession", directly.

Methods

browserView(object, segment = genomeSegment(object), track = tracks(object), ...)
Creates a browserView of segment with visible tracks named in track. Arguments in ... correspond to slots in the genomeSegment class and override those in segment.
browserViews(object)
Gets the browserView instances for this session.
genomeSegment(object)
Gets the genomeSegment last displayed in this session.
genomeSequence(object, segment, track = "Assembly")
Gets the sequence in segment and track.
layTrack(object, track, name = names(track), view = TRUE, format = "gff")
Loads a track, stored under name and formatted as format.
trackSet(object, segment = genomeSegment(), name = deparse(substitute(object)), format = "bed", table = NULL)
Retrieves a trackSet with features in segment from track named name. Some built-in tracks have multiple series, each stored in a separate database table. A specific table may be retrieved by passing its name in the table parameter. The exported data is formatted according to format.
tracks(object)
Gets the names of the tracks stored in the session.
ucscTrackModes(object)
Gets the default view modes for the tracks in the session.
ucscTable(object)
Gets the database table in segment from track as a data.frame.

Author(s)

Michael Lawrence

See Also

browserSession for creating instances of this class.


[Package rtracklayer version 1.0.0 Index]