rCGH (version 1.2.0)

segmentCGH: Genomic Profile Segmentation

Description

A function for performing the Log2Ratio segmentation on an object of class "rCGH". See the details section below.

Usage

"segmentCGH"(object, Smooth=TRUE, UndoSD = NULL,
minLen = 10, nCores=NULL, verbose = TRUE)

Arguments

object

: An object of class "rCGH"

Smooth

: logical. Should the LRR be smoothed before being segmented. See DNAcopy for details.

UndoSD

: numeric. When not specified (default is NULL), the UndoSD value is estimated from the Log2Ratios. See DNAcopy for details.

minLen

: numeric. The minimal length for a segment, in Kb. Shorter segments will be merged to the closest adjacent one. Default value is 10(Kb).

nCores

: numeric. The number of cores to use in order to speed up the computation. When NULL (default), half of the available cores are used. See mclapply.

verbose

: logical. if TRUE (default), progress is printed.

Value

An object of class "rCGH"

Details

This function is a wrapper for the DNAcopy, CNA and segment functions, which allows parallelization and data-driven parameterization. In addition to the usual DNAcopy output, the segmentation table contains the probes Log2Ratio standard deviation for each segment, as well as there length, in Kb.

References

Venkatraman ES1, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data.Bioinformatics. 2007 Mar 15;23(6):657-63.

See Also

CNA, segment, mclapply

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)
st <- getSegTable(cgh)
head(st)