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

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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.

Author
Hoang Tan Nguyen, Tony R Merriman and Mik Black
Date of publication
None
Maintainer
Hoang Tan Nguyen <hoangtannguyenvn@gmail.com>
License
GPL-2
Version
1.12.0
URLs

View on Bioconductor

Man pages

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

Files in this package

CNVrd2/DESCRIPTION
CNVrd2/NAMESPACE
CNVrd2/R
CNVrd2/R/AllClasses.R
CNVrd2/R/AllGenerics.R
CNVrd2/R/calculateLDSNPandCNV.R
CNVrd2/R/countReadInWindow.R
CNVrd2/R/emnormalCNV.R
CNVrd2/R/groupBayesianCNVs.R
CNVrd2/R/groupCNVs.R
CNVrd2/R/identifyPolymorphicRegion.R
CNVrd2/R/plotCNVrd2.R
CNVrd2/R/plotPolymorphicRegion.R
CNVrd2/R/searchGroupCNVs.R
CNVrd2/R/segmentSamples.R
CNVrd2/R/segmentSamplesUsingPopInformation.R
CNVrd2/build
CNVrd2/build/vignette.rds
CNVrd2/data
CNVrd2/data/ccl3l1data.txt.gz
CNVrd2/data/fcgr3bMXL.RData
CNVrd2/inst
CNVrd2/inst/doc
CNVrd2/inst/doc/CNVrd2.R
CNVrd2/inst/doc/CNVrd2.Rnw
CNVrd2/inst/doc/CNVrd2.pdf
CNVrd2/inst/extdata
CNVrd2/inst/extdata/ccl3l1data.txt
CNVrd2/inst/extdata/chr1.161600000.161611000.vcf.gz
CNVrd2/inst/extdata/chr1.161600000.161611000.vcf.gz.tbi
CNVrd2/inst/extdata/chr17.34800000.34830000.vcf.gz
CNVrd2/inst/extdata/chr17.34800000.34830000.vcf.gz.tbi
CNVrd2/inst/extdata/chr17.34815000.34823000.vcf.gz
CNVrd2/inst/extdata/chr17.34815000.34823000.vcf.gz.tbi
CNVrd2/man
CNVrd2/man/CNVrd2-class.Rd
CNVrd2/man/CNVrd2-package.Rd
CNVrd2/man/calculateLDSNPandCNV.Rd
CNVrd2/man/ccl3l1data.Rd
CNVrd2/man/clusteringCNVs-class.Rd
CNVrd2/man/countReadInWindow-methods.Rd
CNVrd2/man/countReadInWindow.Rd
CNVrd2/man/emnormalCNV-methods.Rd
CNVrd2/man/emnormalCNV.Rd
CNVrd2/man/fcgr3bMXL.Rd
CNVrd2/man/groupBayesianCNVs.Rd
CNVrd2/man/groupCNVs-methods.Rd
CNVrd2/man/groupCNVs.Rd
CNVrd2/man/identifyPolymorphicRegion-methods.Rd
CNVrd2/man/identifyPolymorphicRegion.Rd
CNVrd2/man/numericOrNULL-class.Rd
CNVrd2/man/plotCNVrd2-methods.Rd
CNVrd2/man/plotCNVrd2.Rd
CNVrd2/man/plotPolymorphicRegion-methods.Rd
CNVrd2/man/plotPolymorphicRegion.Rd
CNVrd2/man/searchGroupCNVs-methods.Rd
CNVrd2/man/searchGroupCNVs.Rd
CNVrd2/man/segmentSamples-methods.Rd
CNVrd2/man/segmentSamples.Rd
CNVrd2/man/segmentSamplesUsingPopInformation-methods.Rd
CNVrd2/man/segmentSamplesUsingPopInformation.Rd
CNVrd2/man/vectorORfactor-class.Rd
CNVrd2/vignettes
CNVrd2/vignettes/CNVrd2.Rnw
CNVrd2/vignettes/refCNVrd2.bib