segmentCGH {rCGH} | R Documentation

## Genomic Profile Segmentation

### Description

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

### Usage

    ## S4 method for signature '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.

### 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.

### Value

An object of class `"rCGH"`

### Author(s)

Frederic Commo

### 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 <- segmentCGH(cgh, nCores=1)
    st <- getSegTable(cgh)
    head(st)

[Package rCGH version 1.20.0 Index]