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, range = range(object), track = trackNames(object), ...)
Creates a BrowserView of range with visible tracks specified by track. track may be an instance of UCSCTrackModes. Arguments in ... should override slots in range 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.
range(x)
Gets the RangesList last displayed in this session.
genome(x)
Gets the genome identifier of the session, i.e. genome(range(x)).
range(x) <- value
Sets value, a RangesList, as the range of session x. Note that this setting only lasts until a view is created or manipulated. This mechanism is useful, for example, when treating the UCSC browser as a database, rather than a genome viewer.
genome(x) <- value
Sets the genome identifier on the range of session x.
getSeq(object, range, track = "Assembly")
Gets the sequence in range and track.
track(object, name = names(track), view = TRUE, format = "gff", ...) <- value
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 TrackLine subclass or parameters to pass on to the export function for format.
track(object, name, range = range(object), table = NULL)
Retrieves a RangedData with features in range 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. See tableNames for a way to list the available tables.
trackNames(object)
Gets the names of the tracks stored in the session.
ucscTrackModes(object)
Gets the default view modes for the tracks in the session.

Author(s)

Michael Lawrence

See Also

browserSession for creating instances of this class.


[Package rtracklayer version 1.4.1 Index]