class:TrackDb

TrackDb-class

$,TrackDb-method

$<-,TrackDb-method

[[,TrackDb,ANY,ANY-method

[[<-,TrackDb,ANY,ANY-method

track<-,TrackDb,ANY-method


  The <code>TrackDb</code> class is an abstraction around a database of
  tracks. Implementations include <code>BrowserSession</code>
  derivatives and <code>QuickloadGenome</code>. Here, a track is
  defined as an interval dataset.


classes

methods

Extensible framework for interacting with multiple genome
browsers (currently UCSC built-in) and manipulating
annotation tracks in various formats (currently GFF, BED, bedGraph, BED15,
WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the
supported browsers, as well as query and modify the browser state, such as the
current viewport.

Michael Lawrence

rtracklayer

R interface to genome browsers and their annotation tracks

TrackDb-class function

Every implementation should support these methods: <dl>
    <dt></dt><dd>
      <code>length(x)</code>: number of tracks
    </dd> <dt></dt><dd>
      <code>names(x)</code>, <code>trackNames(x)</code>: names of the tracks
    </dd> <dt></dt><dd>
      <code>mcols(x)</code>: merged metadata on the tracks
    </dd> <dt></dt><dd>
      <code>track(x, name)</code>, <code>x$name</code>, <code>x[[name]]</code>:
      get the track called <code>name</code>
    </dd> <dt></dt><dd>
      <code>track(x, name) &lt;- value</code>, <code>x$name &lt;- value</code>,
      <code>x[[name]] &lt;- value</code>: store the track <code>value</code> under
      <code>name</code>. Different implementations will support different
      types for <code>value</code>. Generally, an interval data structure like
      <code>GenomicRanges</code>.
    </dd> </dl> 

Accessor Methods

Track Databases

TrackDb-class: Track Databases

Description

Arguments

Accessor Methods