| 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, segment =
genomeSegment(object), track = tracks(object), ...)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)browserView instances for this session. genomeSegment(object)genomeSegment last displayed in this session. genomeSequence(object, segment, track = "Assembly")segment and track.
layTrack(object, track, name = names(track),
view = TRUE, format = "gff", ...)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)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)ucscTrackModes(object)ucscTable(object)table
in segment from track as a data.frame. Michael Lawrence
browserSession for creating instances of this class.