recenter: Recentering a Genomic Profile

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

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)

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