browserSession-class: Class "BrowserSession"
In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description Objects from the Class Methods Author(s) See Also

An object representing a genome browser session. As a derivative of TrackDb, each session contains a set of loaded tracks. In addition, it has a set of views, in the form of BrowserView instances, on those tracks. Note that this is a virtual class; a concrete implementation is provided by each backend driver.

A virtual Class: No objects may be created from it. See browserSession for obtaining an instance of an implementation for a particular genome browser.

This specifies the API implemented by each browser backend. Note that a backend is not required to support all operations, and that each backend often has additional parameters for each of the methods. See the backend-specific documentation for more details. The only built-in backend is UCSCSession.

If a method is denoted as virtual, it must be implemented by the backend to support the corresponding feature. Otherwise, the fallback behavior is described.

virtual browserView(object, range = range(object), track = trackNames(object), ...): Constructs a BrowserView of range for this session.
virtual browserViews(object, ...): Gets the BrowserView instances belonging to this session.
activeView(object, ...): Returns the BrowserView that is currently active in the session. Fallback calls browserViews and queries each view with activeView.
range(x, ...): Gets the GRanges representing the range of the genome currently displayed by the browser (i.e. the range shown by the active view) or a default value (possibly NULL) if no views exist.
virtual getSeq(object, range = range(object), ...): gets a genomic sequence of range from this session.
virtual sequence(object, ...) <- value: Loads a sequence into the session.
virtual track(object, name = deparse(substitute(track)), view = TRUE, ...) <- value: Loads one or more tracks into the session and optionally open a view of the track.
x[[i]] <- value: Loads the track value into session x, under the name i. Shortcut to above.
x$name <- value: Loads the track value into session x, under the name name. Shortcut to above.
virtual track(object, ...): Gets a track from a session.
x[[i]]: Gets the track named i from session x. A shortcut to track.
x$name: Gets the track named name from session x. A shortcut to track.
virtual trackNames(object, ...): Gets the names of the tracks stored in this session.
virtual genome(x), genome(x) <- value: Gets or sets the genome identifier (e.g. “hg18”) for the session.
virtual close(con, ...): Close this session.
show(object, ...): Output a textual description of this session.