BrowserSession-class {rtracklayer}R Documentation

Class "BrowserSession"

Description

An object representing a genome browser session. Each session corresponds to a set of loaded tracks and a set of BrowserView instances. Note that this is a virtual class; a concrete implementation is provided by each backend driver.

Objects from the Class

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

Methods

This specifies the API implemented by each browser backend. Note that a backend is not guaranteed 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.

browserView(object, range = range(object), track = trackNames(object), ...)
Constructs a BrowserView of range for this session.
browserViews(object, ...)
Gets the BrowserView instances belonging to this session.
activeView(object, ...)
Returns the BrowserView that is currently active in the session.
range(x, ...)
Gets the RangesList 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.
getSeq(object, range = range(object), ...)
gets a genomic sequence of range from this session.
sequence(object, ...) <- value
Loads a sequence into the session.
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$name <- value
Loads the track value into session x, under the name name. Shortcut to above.
track(object, ...)
Gets a track from a session as a RangedData.
x[[i]]
Gets the track named i from session x. A shortcut to track.
x$name
Gets the track named name from session x. A shortcut to track.
trackNames(object, ...)
Gets the names of the tracks stored in this session.
close(con, ...)
Close this session.
show(object, ...)
Output a textual description of this session.

Author(s)

Michael Lawrence

See Also

browserSession for obtaining implementations of this class for a particular genome browser.


[Package rtracklayer version 1.4.1 Index]