Package: CNVrd2 1.45.0

Hoang Tan Nguyen

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

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.

Authors:Hoang Tan Nguyen, Tony R Merriman and Mik Black

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CNVrd2.pdf |CNVrd2.html✨
CNVrd2/json (API)

# Install 'CNVrd2' in R:

install.packages('CNVrd2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hoangtn/cnvrd2/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

ccl3l1data - Data of CCL3L1 gene
copynumberGroups - MXL population data
objectCNVrd2 - MXL population data
resultSegment - MXL population data

On BioConductor:CNVrd2-1.45.0(bioc 3.21)CNVrd2-1.44.0(bioc 3.20)

copynumbervariation snp sequencing software coverage linkagedisequilibrium clustering.jags cpp

4.92 score 3 stars 230 downloads 7 mentions 11 exports 94 dependencies

Last updated 2 months agofrom:55815ed7ca. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:calculateLDSNPandCNV countReadInWindow emnormalCNV groupBayesianCNVs groupCNVs identifyPolymorphicRegion plotCNVrd2 plotPolymorphicRegion searchGroupCNVs segmentSamples segmentSamplesUsingPopInformation

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli coda codetools colorspace cpp11 crayon curl DBI DelayedArray DNAcopy fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png R6 RColorBrewer RCurl restfulr Rhtslib rjags rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

A Markdown Vignette with knitr

Rendered fromCNVrd2.Rnwusingknitr::knitron Nov 29 2024.

Last update: 2014-11-13
Started: 2013-10-31

Citation

Development and contributors

Readme and manuals

Help Manual

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