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.