segmentSamples: Implement the segmentation process

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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. [e-mail]

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)

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.