plotDensity {rCGH} | R Documentation

## 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

    ## 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)

[Package rCGH version 1.20.0 Index]