Man pages for rCNV
Detect Copy Number Variants from SNPs Data
| 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... |
| alleleINF | Allele info example data |
| allele.info | Get allele information for duplicate detection |
| cnv | Find CNVs from deviants |
| cpm.normal | Calculate normalized depth for alleles |
| depthVsSample | Simulate median allele ratios for varying number of samples... |
| dupGet | Detect deviants from SNPs; classify SNPs |
| dup.plot | Plot classified SNPs into deviants/CNVs and... |
| dup.validate | Validate detected deviants/cnvs |
| exportVCF | Export VCF files |
| get.miss | Get missingness of individuals in raw vcf |
| gt.format | Format genotype for BayEnv and BayPass |
| hetTgen | Generate allele depth or genotype table |
| h.zygosity | Determine per sample heterozygosity and inbreeding... |
| 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... |
| vst | Calculate population-wise Vst |
| vstPermutation | Run permutation on Vst |
