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` 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.

[Package rtracklayer version 1.48.0 Index]