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CNVrd2 (version 1.10.2)

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

Description

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.

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Version

Version

1.10.2

License

GPL-2

Issues

1

Pull Requests

0

Stars

3

Forks

3

Maintainer

Hoang Tan Nguyen

Last Published

February 15th, 2017

Functions in CNVrd2 (1.10.2)

plotCNVrd2-methods

Method plotCNVrd2
countReadInWindow

Obtain read counts in constant windows.
emnormalCNV-methods

Method emnormalCNV
CNVrd2-class

Class "CNVrd2"
identifyPolymorphicRegion

Identity polymorphic regions.
calculateLDSNPandCNV

calculateLDSNPandCNV
clusteringCNVs-class

Class "clusteringCNVs"
segmentSamples-methods

Method segmentSamples
CNVrd2-package

CNVrd2
segmentSamplesUsingPopInformation

Implement the segmentation process for multiple populations
identifyPolymorphicRegion-methods

Methods for Function identifyPolymorphicRegion
countReadInWindow-methods

Method countReadInWindow
plotPolymorphicRegion

Plot polymorphic regions.
vectorORfactor-class

Class "vectorORfactor"
plotCNVrd2

Plot traces of samples.
groupCNVs-methods

Method groupCNVs
groupCNVs

Cluster segmentation scores into groups.
searchGroupCNVs-methods

Method searchGroupCNVs
segmentSamples

Implement the segmentation process
plotPolymorphicRegion-methods

Methods for Function plotPolymorphicRegion
emnormalCNV

Implement the EM algorithm
searchGroupCNVs

Choose a number of CN groups
groupBayesianCNVs

groupBayesianCNVs
fcgr3bMXL

MXL population data (The 1000 Genomes Project)
numericOrNULL-class

Class "numericOrNULL"
ccl3l1data

Data of CCL3L1 gene (The 1000 Genomes Project)
segmentSamplesUsingPopInformation-methods

Method segmentSamplesUsingPopInformation