rCGH (version 1.2.2)

plotDensity: Visualizing the Log2Ratios Density and Centralization Decision

Description

This function display the distribution of the Log2Ratios, as well as how the "EMnormalize" step estimates the mixture of gaussian populations, and choose a centralization value.

Usage

## S3 method for class 'rCGH':
plotDensity(object, breaks=NULL, Title=NULL,...)

Arguments

object

: An object of class "rCGH"

breaks

: The number of breaks to use. See hist. When NULL (default), breaks is arbitrarily defined from the number of values to draw.

Title

: character string. A title for the density plot. If NULL (default), the sample name (when exists) will be used.

...

: Other graphical parameters supported by par.

Value

• None.

See Also

plotProfile, plotLOH, multiplot, view

Examples

filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
    package = "rCGH")
cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")
cgh <- adjustSignal(cgh, nCores=1)
cgh <- EMnormalize(cgh)
plotDensity(cgh)