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


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Documentation for package ‘CNVrd2’ version 1.45.0

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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"'