CNVice (Inbreeding Coefficients Estimation for CNV data) is a freely available R script for population genetics applications. CNVice performs the following analyses:
- Estimates allele frequencies for a given population assuming Hardy-Weinberg equilibrium (HWE), using the expectation maximization algorithm as implemented in CoNVEM (Gaunt et al. 2010), conditioning on the observed diplotype frequencies.
- Estimates the population structure parameter CNV and allele frequencies, using the profiled likelihood function and the Expectation Maximization (EM) algorithm (Dempster et al. 1977)
- Estimates the population genotype frequency, conditioning on the observed diplotype distribution and the estimated fCNV and allele frequencies.
- Uses trio information to improve the inference of an offspring’s genotype, by considering the parents’ diplotypes and the population genotype frequency.
Citing us: the CNVice paper has been submitted for publication and will be soon available here.
#Requirements CNVice is implemented in R. Packages aylmer and hwriter are installed when CNVice is executed.
#Input The main input for CNVice is the distribution of observed diplotype frequencies of a given loci in a population. The distribution must always start with diplotype 0 (see the Examples section).
#Running CNVice The main function to be executed is: executeCnvice(Nj,fpar,rept,document)
Please read the user guide for more details.