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 1.24.0 Index]