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) <- value
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
x
.getSeq(object, range, track = "Assembly")
range
and track
.
track(object, name = names(track),
view = TRUE, format = "gff", ...) <- value
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)
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.