plotDensity: Visualizing the Log2Ratios Density and Centralization...

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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

## S4 method for signature '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.

Author(s)

Frederic Commo

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 <- segmentCGH(cgh, nCores=1)
cgh <- EMnormalize(cgh)
plotDensity(cgh)

rCGH documentation built on Nov. 8, 2020, 8:30 p.m.