wigTrackLine-class {rtracklayer}R Documentation

Class "wigTrackLine"

Description

A UCSC track line for Wiggle tracks.

Objects from the Class

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

Slots

altColor:
Object of class "integer" giving an alternate color, as from col2rgb.
autoScale:
Object of class "logical" indicating whether to automatically scale to min/max of the data.
gridDefault:
Object of class "logical" indicating whether a grid should be drawn.
maxHeightPixels:
Object of class "numeric" of length three (max, default, min), giving the allowable range for the vertical height of the graph.
graphType:
Object of class "character", specifying the graph type, either "bar" or "points".
viewLimits:
Object of class "numeric" and of length two specifying the data range (min, max) shown in the graph.
yLineMark:
Object of class "numeric" giving the position of a horizontal line.
yLineOnOff:
Object of class "logical" indicating whether the yLineMark should be visible.
windowingFunction:
Object of class "character", one of "maximum", "mean", "minimum", for removing points when the graph shrinks.
smoothingWindow:
Object of class "numeric" giving the window size of a smoother to pass over the graph.
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).
priority:
Object of class "numeric" specifying the rank of this track.

Extends

Class "ucscTrackLine", directly.

Methods

as(object, "character")
Export line to its string representation.
as(object, "basicTrackLine")
Convert this line to a basic UCSC track line, using defaults for slots not held in common.

Author(s)

Michael Lawrence

References

Official documentation: http://genome.ucsc.edu/goldenPath/help/wiggle.html.

See Also

export.wig for exporting tracks in the Wiggle format.


[Package rtracklayer version 1.2.2 Index]