# Detect Copy Number Variants from SNPs Data

## Documentation for package ‘rCNV’ version 1.3.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

ad.correct | Correct allele depth values
ADnorm | Normalized allele depth example data
ADtable | Allele Depth (AD) example data
allele.freq | Generate allele frequency table for individuals or populations
allele.info | Get allele information for duplicate detection
alleleINF | Allele info example data
cnv | Find CNVs from deviants
cpm.normal | Calculate normalized depth for alleles
depthVsSample | Simulate median allele ratios for varying number of samples and depth values
dup.plot | Plot classified SNPs into deviants/CNVs and non-deviants/non-CNVs
dup.validate | Validate detected deviants/cnvs
dupGet | Detect deviants from SNPs; classify SNPs
exportVCF | Export VCF files
get.miss | Get missingness of individuals in raw vcf
gt.format | Format genotype for BayEnv and BayPass
h.zygosity | Determine per sample heterozygosity and inbreeding coefficient
hetTgen | Generate allele depth or genotype table
maf | Remove MAF allele
norm.fact | Calculate normalization factor for each sample
power.bias | Simulate and plot detection power of bias in allele ratios
readVCF | Import VCF file
relatedness | Determine pairwise relatedness
sig.hets | Identify significantly different heterozygotes from SNPs data
sim.als | Simulate Allele Frequencies
vcf.stat | Get sequencing quality statistics of raw VCF files (with GatK generated vcf files only)
vst | Calculate population-wise Vst
vstPermutation | Run permutation on Vst