Detect Copy Number Variants from SNPs Data

Documentation for package ‘rCNV’ version 1.1.0

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 duplicates
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