ucscView-class: Class "UCSCView"

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

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 or IntegerRangesList 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. The value may be either a UCSCTrackModes instance or a character vector that will be coerced by a call to ucscTrackModes.

Utilities

viewURL(x)

Gets the URL corresponding to the view x. Typically used when passing browse=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.

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.