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

---

Documentation for package ‘CNVrd2’ version 1.47.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

CNVrd2-package	CNVrd2
.Random.seed	MXL population data (The 1000 Genomes Project)
allGroups	MXL population data (The 1000 Genomes Project)
bamFiles	MXL population data (The 1000 Genomes Project)
calculateLDSNPandCNV	calculateLDSNPandCNV
ccl3l1data	Data of CCL3L1 gene (The 1000 Genomes Project)
clusteringCNVs-class	Class '"clusteringCNVs"'
CNVrd2-class	Class '"CNVrd2"'
copynumberGroups	MXL population data (The 1000 Genomes Project)
countReadInWindow	Obtain read counts in constant windows.
countReadInWindow-method	Class '"CNVrd2"'
countReadInWindow-methods	Method 'countReadInWindow'
emnormalCNV	Implement the EM algorithm
emnormalCNV-method	Class '"clusteringCNVs"'
emnormalCNV-methods	Method 'emnormalCNV'
fcgr3bMXL	MXL population data (The 1000 Genomes Project)
groupBayesianCNVs	groupBayesianCNVs
groupCNVs	Cluster segmentation scores into groups.
groupCNVs-method	Class '"clusteringCNVs"'
groupCNVs-methods	Method 'groupCNVs'
identifyPolymorphicRegion	Identity polymorphic regions.
identifyPolymorphicRegion-method	Methods for Function 'identifyPolymorphicRegion'
identifyPolymorphicRegion-methods	Methods for Function 'identifyPolymorphicRegion'
numericOrNULL-class	Class '"numericOrNULL"'
objectCluster	Class '"clusteringCNVs"'
objectCNVrd2	MXL population data (The 1000 Genomes Project)
plotCNVrd2	Plot traces of samples.
plotCNVrd2-method	Class '"CNVrd2"'
plotCNVrd2-methods	Method 'plotCNVrd2'
plotPolymorphicRegion	Plot polymorphic regions.
plotPolymorphicRegion-method	Methods for Function 'plotPolymorphicRegion'
plotPolymorphicRegion-methods	Methods for Function 'plotPolymorphicRegion'
readCountMatrix	MXL population data (The 1000 Genomes Project)
resultSegment	MXL population data (The 1000 Genomes Project)
searchGroupCNVs	Choose a number of CN groups
searchGroupCNVs-method	Class '"clusteringCNVs"'
searchGroupCNVs-methods	Method 'searchGroupCNVs'
segmentSamples	Implement the segmentation process
segmentSamples-method	Method 'segmentSamples'
segmentSamples-methods	Method 'segmentSamples'
segmentSamplesUsingPopInformation	Implement the segmentation process for multiple populations
segmentSamplesUsingPopInformation-method	Method 'segmentSamplesUsingPopInformation'
segmentSamplesUsingPopInformation-methods	Method 'segmentSamplesUsingPopInformation'
vectorORfactor-class	Class '"vectorORfactor"'