| UCSCSession-class {rtracklayer} | R Documentation |
An implementation of BrowserSession
for the UCSC genome browser.
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.
url:"character" holding the
base URL of the UCSC browser. hguid:"numeric" holding the
user identification code.views:"environment" containing
a list stored under the name "instances". The list holds the instances of
BrowserView for this session.
Class "BrowserSession", directly.
browserView(object, range =
range(object), track = trackNames(object), ...)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)BrowserView instances for this session. range(x)RangesList last
displayed in this session. genome(x)genome(range(x)).range(x) <- valuevalue, 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) <- valuex.getSeq(object, range, track = "Assembly")range and track.
track(object, name = names(track),
view = TRUE, format = "gff", ...) <- valuename 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)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)ucscTrackModes(object)Michael Lawrence
browserSession for creating instances of this class.