rCGH (version 1.2.2)

segmentCGH: Genomic Profile Segmentation

Description

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

Usage

## S3 method for class 'rCGH':
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

http://www.ncbi.nlm.nih.gov/pubmed/17234643{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)