Calculating Likelihoods by Pedigree Paring

Documentation for package ‘clipp’ version 1.1.1

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