BrowserSession-class {rtracklayer} | R Documentation

## Class "BrowserSession"

### Description

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.

### 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 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 `track`s 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.

### Author(s)

Michael Lawrence

### See Also

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

[Package rtracklayer version 1.52.1 Index]