CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
Version 1.14.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorHoang Tan Nguyen, Tony R Merriman and Mik Black
Bioconductor views Clustering. CopyNumberVariation Coverage LinkageDisequilibrium SNP Sequencing Software
Date of publicationNone
MaintainerHoang Tan Nguyen <hoangtannguyenvn@gmail.com>
LicenseGPL-2
Version1.14.0
URL https://github.com/hoangtn/CNVrd2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNVrd2")

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"'

Functions

.Random.seed Man page
CNVrd2-class Man page
CNVrd2-package Man page
allGroups Man page
bamFiles Man page
calculateLDSNPandCNV Man page Source code
ccl3l1data Man page
clusteringCNVs-class Man page
copynumberGroups Man page
countReadInWindow Man page
countReadInWindow,CNVrd2-method Man page
countReadInWindow-methods Man page
emnormalCNV Man page
emnormalCNV,clusteringCNVs-method Man page
emnormalCNV-methods Man page
fcgr3bMXL Man page
groupBayesianCNVs Man page Source code
groupCNVs Man page
groupCNVs,clusteringCNVs-method Man page
groupCNVs-methods Man page
identifyPolymorphicRegion Man page
identifyPolymorphicRegion,CNVrd2-method Man page
identifyPolymorphicRegion-methods Man page
numericOrNULL-class Man page
objectCNVrd2 Man page
objectCluster Man page
plotCNVrd2 Man page
plotCNVrd2,CNVrd2-method Man page
plotCNVrd2-methods Man page
plotPolymorphicRegion Man page
plotPolymorphicRegion,CNVrd2-method Man page
plotPolymorphicRegion-methods Man page
readCountMatrix Man page
resultSegment Man page
searchGroupCNVs Man page
searchGroupCNVs,clusteringCNVs-method Man page
searchGroupCNVs-methods Man page
segmentSamples Man page
segmentSamples,CNVrd2-method Man page
segmentSamples-methods Man page
segmentSamplesUsingPopInformation Man page
segmentSamplesUsingPopInformation,CNVrd2-method Man page
segmentSamplesUsingPopInformation-methods Man page
vectorORfactor-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/calculateLDSNPandCNV.R
R/countReadInWindow.R
R/emnormalCNV.R
R/groupBayesianCNVs.R
R/groupCNVs.R
R/identifyPolymorphicRegion.R
R/plotCNVrd2.R
R/plotPolymorphicRegion.R
R/searchGroupCNVs.R
R/segmentSamples.R
R/segmentSamplesUsingPopInformation.R
build
build/vignette.rds
data
data/ccl3l1data.txt.gz
data/fcgr3bMXL.RData
inst
inst/doc
inst/doc/CNVrd2.R
inst/doc/CNVrd2.Rnw
inst/doc/CNVrd2.pdf
inst/extdata
inst/extdata/ccl3l1data.txt
inst/extdata/chr1.161600000.161611000.vcf.gz
inst/extdata/chr1.161600000.161611000.vcf.gz.tbi
inst/extdata/chr17.34800000.34830000.vcf.gz
inst/extdata/chr17.34800000.34830000.vcf.gz.tbi
inst/extdata/chr17.34815000.34823000.vcf.gz
inst/extdata/chr17.34815000.34823000.vcf.gz.tbi
man
man/CNVrd2-class.Rd
man/CNVrd2-package.Rd
man/calculateLDSNPandCNV.Rd
man/ccl3l1data.Rd
man/clusteringCNVs-class.Rd
man/countReadInWindow-methods.Rd
man/countReadInWindow.Rd
man/emnormalCNV-methods.Rd
man/emnormalCNV.Rd
man/fcgr3bMXL.Rd
man/groupBayesianCNVs.Rd
man/groupCNVs-methods.Rd
man/groupCNVs.Rd
man/identifyPolymorphicRegion-methods.Rd
man/identifyPolymorphicRegion.Rd
man/numericOrNULL-class.Rd
man/plotCNVrd2-methods.Rd
man/plotCNVrd2.Rd
man/plotPolymorphicRegion-methods.Rd
man/plotPolymorphicRegion.Rd
man/searchGroupCNVs-methods.Rd
man/searchGroupCNVs.Rd
man/segmentSamples-methods.Rd
man/segmentSamples.Rd
man/segmentSamplesUsingPopInformation-methods.Rd
man/segmentSamplesUsingPopInformation.Rd
man/vectorORfactor-class.Rd
vignettes
vignettes/CNVrd2.Rnw
vignettes/refCNVrd2.bib
CNVrd2 documentation built on May 20, 2017, 10:50 p.m.