R: Calculating Likelihoods by Pedigree Paring

# Calculating Likelihoods by Pedigree Paring

## Documentation for package ‘clipp’ version 1.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

clipp-package | clipp: Calculate Likelihoods by Pedigree Paring
clipp | clipp: Calculate Likelihoods by Pedigree Paring
combine_loci | Combine the genotype frequencies and transition matrices of two genetic loci
dat_large | Simulated data on one family with approximately 10,000 members
dat_small | Simulated data on 10 families with approximately 100 members each
genotype_probabilities | Calculate genotype probabilities for a target person
geno_freq_monogenic | Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium
geno_freq_phased | Calculate phased genotype frequencies from allele frequencies, assuming Hardy-Weinberg equilibrium
geno_freq_polygenic | Genotype frequencies for the hypergeometric polygenic model
pedigree_loglikelihood | Calculate the log-likelihoods of pedigrees
penet_large | A penetrance matrix relating the phenotypes in 'dat_large' to three genotypes
penet_small | A penetrance matrix relating the phenotypes of 'dat_small' to three genotypes
trans_monogenic | The transmission matrix for a single genetic locus
trans_phased | The transmission matrix for phased genotypes
trans_polygenic | The transmission matrix for the hypergeometric polygenic model