BasicTrackLine-class {rtracklayer} | R Documentation

## Class "BasicTrackLine"

### Description

The type of UCSC track line used to annotate most types of tracks (every type except Wiggle).

### Objects from the Class

Objects can be created by calls of the form `new("BasicTrackLine", ...)` or parsed from a character vector track line with `as(text, "BasicTrackLine")` or converted from a `GraphTrackLine` using `as(wig, "BasicTrackLine")`.

### Slots

`itemRgb`:

  Object of class `"logical"` indicating whether each feature in a track uploaded as BED should be drawn in its specified color.

`useScore`:

  Object of class `"logical"` indicating whether the data value should be mapped to color.

`group`:

  Object of class `"character"` naming a group to which this track should belong.

`db`:

  Object of class `"character"` indicating the associated genome assembly.

`offset`:

  Object of class `"numeric"`, a number added to all positions in the track.

`url`:

  Object of class `"character"` referring to additional information about this track.

`htmlUrl`:

  Object of class `"character"` referring to an HTML page to be displayed with this track.

`name`:

  Object of class `"character"` specifying the name of the track.

`description`:

  Object of class `"character"` describing the track.

`visibility`:

  Object of class `"character"` indicating the default visible mode of the track, see `UCSCTrackModes`.

`color`:

  Object of class `"integer"` representing the track color (as from `col2rgb`).

`colorByStrand`:

  Object of class `"matrix"` with two columns, as from `col2rgb`. The two colors indicate the color for each strand (positive, negative).

`priority`:

  Object of class `"numeric"` specifying the rank of the track.

### Extends

Class `"TrackLine"`, directly.

### Methods

as(object, "character")

  Export line to its string representation.

as(object, `"GraphTrackLine"`)

  Convert this line to a graph track line, using defaults for slots not held in common.

### Author(s)

Michael Lawrence

### References

http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK for the official documentation.

### See Also

`GraphTrackLine` for Wiggle/bedGraph tracks.

[Package rtracklayer version 1.52.1 Index]