segmentSamples {CNVrd2} | R Documentation

## Implement the segmentation process

### Description

Segment read-count windows into region having similar signal values by using the DNAcopy package (Venkatraman and Olshen, 2007) and refine this process to obtain segmentation scores at genes.

### Usage

    segmentSamples(Object, ...)

### Arguments

`Object` | An object of class CNVrd2.
`...` | Optional arguments.

### Value

`segmentResults` | All results of the segmentation process.
`segmentationScores` | Segmentation scores of the gene(s) being measured.
`observedReadCountRatios` | Observed read-count ratios of genes. This value is a matrix of observed read-count ratios at genes if (only inputBamFile = TRUE).
`stdCntMatrix` | Matrix of read counts (standardized).

### Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com

### References

Venkatraman, E., Olshen, A. B., 2007. A faster circular binary segmentation algorithm for the analysis of array chg data. Bioinformatics 23 (6), 657-663.

### See Also

`countReadInWindow`, `DNAcopy`

### Examples

    data(fcgr3bMXL)
    ## Not run: resultSegment <- segmentSamples(Object = objectCNVrd2, stdCntMatrix = readCountMatrix)

[Package CNVrd2 version 1.18.0 Index]