# 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 1.16.0

- 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"'