UCSCView-class {rtracklayer} | R Documentation |
Class "UCSCView"
Description
An object representing a view of a genome in the UCSC browser.
Objects from the Class
Calling browserView(session, range = range(object), track
= trackNames(object), browse = TRUE, ...)
creates BrowserView
of range
with visible
tracks specified by track
. track
may be an instance of
UCSCTrackModes
. Arguments in ...
should
match parameters to a
ucscTrackModes
method for creating a
UCSCTrackModes
instance that will be merged with and override
modes indicated by the track
parameter. If browse
is
TRUE
(default), automatically launch a browser to display the
view.
Slots
hgsid
:Object of class
"numeric"
, which identifies this view to UCSC.session
:Object of class
"BrowserSession"
to which this view belongs.
Extends
Class "BrowserView"
, directly.
Methods
activeView(object)
Obtains a logical indicating whether this view is the active view.
range(object)
Obtains the
GRanges
displayed by this view.range(object) <- value
Sets the
GRanges
orIntegerRangesList
displayed by this view.trackNames(object)
Gets the names of the visible tracks in this view.
trackNames(object) <- value
Sets the visible tracks by name.
visible(object)
Get a named logical vector indicating whether each track is visible.
visible(object) <- value
Set a logical vector indicating the visibility of each track, in the same order as returned by
visible(object)
.ucscTrackModes(object)
Obtains the
UCSCTrackModes
for this view.ucscTrackModes(object) <- value
Sets the
UCSCTrackModes
for this view. Thevalue
may be either aUCSCTrackModes
instance or a character vector that will be coerced by a call toucscTrackModes
.
Utilities
- viewURL(x)
Gets the URL corresponding to the view
x
. Typically used when passingbrowse=FALSE
to the constructor in order to display the view in another way.
Author(s)
Michael Lawrence
See Also
browserView
for creating instances of this class.