Package: rCNV 1.5.900

rCNV: Detect Copy Number Variants from SNPs Data

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

Authors:Piyal Karunarathne [aut, cre], Qiujie Zhou [aut], Klaus Schliep [aut], Pascal Milesi [aut]

rCNV_1.5.900.tar.gz
rCNV_1.5.900.zip(r-4.7)rCNV_1.5.900.zip(r-4.6)rCNV_1.5.900.zip(r-4.5)
rCNV_1.5.900.tgz(r-4.6-any)rCNV_1.5.900.tgz(r-4.5-any)
rCNV_1.5.900.tar.gz(r-4.7-any)rCNV_1.5.900.tar.gz(r-4.6-any)
rCNV_1.5.900.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rCNV/json (API)
NEWS

# Install 'rCNV' in R:

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

Bug tracker:https://github.com/piyalkarum/rcnv/issues

Pkgdown/docs site:https://piyalkarum.github.io

Datasets:

ADnorm - Normalized allele depth example data
ADtable - Allele Depth (AD) example data
alleleINF - Allele info example data

On CRAN:

genomicvariation sequencing copynumbervariation cnv-analysis copy-number-variation gene-duplication genetics genomics landscape-genetics snps

3.78 score 6 stars 7 scripts 166 downloads 27 exports 130 dependencies

Last updated from:81c225fc0f. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	366
source / vignettes	OK	358
linux-release-x86_64	NOTE	346
macos-release-arm64	NOTE	316
macos-oldrel-arm64	NOTE	355
windows-devel	NOTE	308
windows-release	NOTE	266
windows-oldrel	NOTE	284
wasm-release	OK	172

Exports:ad.correct allele.freq allele.info allele.info.WGS allele.info.WGS.GCcor allele.info.WGS3 cnv cpm.normal depthVsSample dup.plot dup.validate dupGet exportVCF get.miss gt.format h.zygosity hetTgen maf norm.fact power.bias readVCF relatedness sig.hets sim.als vcf.stat vst vstPermutation

Dependencies:abind askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops bslib cachem checkmate cigarillo cli cluster codetools colorspace corpcor cpp11 crayon curl data.table DelayedArray digest evaluate extraDistr farver fastmap fdrtool fitdistrplus fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glasso glue GPArotation gridExtra gtable gtools highr Hmisc htmlTable htmltools htmlwidgets httr igraph IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r lattice lavaan lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mnormt nlme nnet numDeriv openssl pbapply pbivnorm pkgconfig plyr png psych qgraph quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment survival sys tinytex UCSC.utils vctrs viridisLite withr xfun XML XVector yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
rCNV: Detect Copy Number Variants from SNP Data	rCNV-package rCNV
Correct allele depth values	ad.correct
Normalized allele depth example data	ADnorm
Allele Depth (AD) example data	ADtable
Generate allele frequency table for individuals or populations	allele.freq
Get allele information for duplicate detection	allele.info
ClrCNV: multicopy detection for WGS	allele.info.WGS
Allele Information with GC-Bias Correction for WGS Data	allele.info.WGS.GCcor
Allele Information for WGS Data (No GC Correction)	allele.info.WGS3
Allele info example data	alleleINF
Find CNVs from deviants	cnv
Calculate normalized depth for alleles	cpm.normal
Simulate median allele ratios for varying number of samples and depth values	depthVsSample
Plot classified SNPs into deviants/CNVs and non-deviants/non-CNVs	dup.plot
Validate detected deviants/cnvs	dup.validate
Detect deviants from SNPs; classify SNPs	dupGet
Export VCF files	exportVCF
Get missingness of individuals in raw vcf	get.miss
Format genotype for BayEnv and BayPass	gt.format
Determine per sample heterozygosity and inbreeding coefficient	h.zygosity
Generate allele depth or genotype table	hetTgen
Remove MAF allele	maf
Calculate normalization factor for each sample	norm.fact
Simulate and plot detection power of bias in allele ratios	power.bias
Import VCF file	readVCF
Determine pairwise relatedness	relatedness
Identify significantly different heterozygotes from SNPs data	sig.hets
Simulate Allele Frequencies	sim.als
Get sequencing quality statistics of raw VCF files (with GatK generated vcf files only)	vcf.stat
Calculate population-wise Vst	vst
Run permutation on Vst	vstPermutation