segmentSamplesUsingPopInformation: Implement the segmentation process for multiple populations

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. Then, the function adjusts segmentation scores for multiple populations using a linear regression model.

Usage

segmentSamplesUsingPopInformation(Object, ...)

Arguments

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

Value

segmentationScores	All adjusted results of the segmentation process.
segmentationScoresFromSinglePops	Segmentation scores of single populations.
segmentResults	Un-adjusted segmentation scores
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

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