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", ...). The arguments in ... correspond to libcurl options, see getCurlHandle. Setting these options may be useful e.g. for getting past a proxy.

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 specified by track. track may be an instance of ucscTrackModes. Arguments in ... should override slots in segment or else match parameters to a ucscTrackModes method for creating a ucscTrackModes instance that will override modes indicated by the track parameter.
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. The arguments in ... are passed on to export.ucsc, so they could be slots in a ucscTrackLine subclass or parameters to pass on to the export function for format.
trackSet(object, segment = genomeSegment(), name = deparse(substitute(object)), 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.
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 1.2.2 Index]