rCGH (version 1.2.2)

recenter<--methods: 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

## S3 method for class '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"

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

# Default peak choice center the profile on the 2nd peak
plotDensity(cgh)

# Recentering on the 3rd density peak
recenter(cgh) <- 3
plotDensity(cgh)