recenter<–methods {rCGH} | R Documentation |
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.
## S4 replacement method for signature 'rCGH' recenter(object) <- value
object |
: An object of class |
value |
: numeric. What peak number to choose to recenter the genomic profile. |
An object of class "rCGH"
When a profile is recentered, the stored workflow parameters are updated.
see getParam
.
Frederic Commo
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)