Learn R Programming

clipp (version 1.1.1)

Calculating Likelihoods by Pedigree Paring

Description

A fast and general implementation of the Elston-Stewart algorithm that can calculate the likelihoods of large and complex pedigrees. References for the Elston-Stewart algorithm are Elston & Stewart (1971) , Lange & Elston (1975) and Cannings et al. (1978) .

Copy Link

Version

Install

install.packages('clipp')

Monthly Downloads

240

Version

1.1.1

License

GPL-3

Maintainer

James Dowty

Last Published

July 12th, 2022

Functions in clipp (1.1.1)

geno_freq_monogenic

Calculate genotype frequencies from allele frequencies using Hardy-Weinberg equilibrium
penet_small

A penetrance matrix relating the phenotypes of dat_small to three genotypes
genotype_probabilities

Calculate genotype probabilities for a target person
geno_freq_polygenic

Genotype frequencies for the hypergeometric polygenic model
trans_monogenic

The transmission matrix for a single genetic locus
clipp-package

clipp: Calculate Likelihoods by Pedigree Paring
combine_loci

Combine the genotype frequencies and transition matrices of two genetic loci
geno_freq_phased

Calculate phased genotype frequencies from allele frequencies, assuming Hardy-Weinberg equilibrium
trans_phased

The transmission matrix for phased genotypes
trans_polygenic

The transmission matrix for the hypergeometric polygenic model
dat_large

Simulated data on one family with approximately 10,000 members
penet_large

A penetrance matrix relating the phenotypes in dat_large to three genotypes
dat_small

Simulated data on 10 families with approximately 100 members each
pedigree_loglikelihood

Calculate the log-likelihoods of pedigrees