segmentSamplesUsingPopInformation

Object


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.<p></p><p>
</p>

methods

CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples,
indentify SNPs tagging copy number variants and detect copy
number polymorphic genomic regions.

Hoang Tan Nguyen

CNVrd2

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

segmentSamplesUsingPopInformation function

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.

Implement the segmentation process for multiple populations

All adjusted results of the segmentation process.

segmentationScores

Segmentation scores of single populations.

segmentationScoresFromSinglePops

segmentResults

Observed read-count ratios of genes. This value is a matrix of observed read-count ratios at genes if (only inputBamFile = TRUE).

segmentSamplesUsingPopInformation: Implement the segmentation process for multiple populations

Description

Usage

Arguments

Value

References

See Also