argoSession-class {rtracklayer} | R Documentation |
An object representing a session in the Argo genome browser.
Objects may be created by calls of the form
browserSession("argo", name, jar)
where name
is
the name of the session in Argo and jar
is the path to the
installed Argo jar file.
jref
:"jobjRef"
holding the
reference to the low-level Argo object. seqcache
:"environment"
that
caches sequence objects after lookup from UCSC.
Class "browserSession"
, directly.
activeView(object)
browserView
for this session. activeView<-(object)
browserView(object, segment =
genomeSegment(object),track = tracks(object, segment, TRUE),
...)
browserView
of
segment
with visible tracks named in
track
. Parameters in ...
correspond to slots in
the genomeSegment
class and override those in
segment
.browserViews(object)
browserView
instances for this session. close(con)
genomeSequence(object, segment)
segment
. laySequence(object, sequence, name, label =
name)
sequence
under name
, labeled as
label
in the user interface. layTrack(object, track, name =
deparse(substitute(track)), view = TRUE)
track
under name
, opening a view of the track if view
is
TRUE
.trackSet(object, name,
segment = genomeSegment(object))
trackSet
named name
from
segment
.tracks(object, segment = NULL, visible =
FALSE)
segment
. If
visible
is TRUE
, only the visible tracks are
returned. Note that in Argo tracks are visible on a
global, not per-session nor per-view, basis.
In order to use this backend, the Argo jar file must be manually
downloaded from the URL in the references. The call to
browserSession
must then pass the path to the jar file
as the jar
parameter. By default, the path is the ‘java’
directory of the rtracklayer package.
Michael Lawrence
The Argo genome browser: http://www.broad.mit.edu/annotation/argo/
browserSession
for creating instances of this class.