recenter<–methods {rCGH} | R Documentation

## Recentering a Genomic Profile

### Description

This function allows the user to recenter a genomic profile stored in an object of class `"rCGH"`.
Peaks are indexed from 1 to k, from left to right, as they appear on the `plotDensity` after the `EMnormalize` step.

### Usage

    ## S4 replacement method for signature 'rCGH'
    recenter(object) <- value

### Arguments

`object` | : An object of class `"rCGH"`
`value` | : numeric. What peak number to choose to recenter the genomic profile.

### Value

An object of class `"rCGH"`

### Note

When a profile is recentered, the stored workflow parameters are updated. see `getParam`.

### Author(s)

Frederic Commo

### See Also

`EMnormalize`, `plotDensity`

### 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)

    # Default peak choice center the profile on the 1st peak
    plotDensity(cgh)

    # Recentering on the 2nd density peak
    recenter(cgh) <- 2
    plotDensity(cgh)

[Package rCGH version 1.16.0 Index]