| clipp-package {clipp} | R Documentation |
clipp: Calculate Likelihoods by Pedigree Paring
Description
clipp provides a fast and general implementation of the Elston-Stewart
algorithm, and can calculate the log-likelihoods of large and complex pedigrees,
including those with loops. General references for the Elston-Stewart algorithm are
(Elston & Stewart, 1971), (Lange & Elston, 1975) and (Cannings et al., 1978).
Details
The main function is pedigree_loglikelihood, which calculates
the pedigree likelihood on page 117 of (Lange, 2002) for almost any choice of
genotype frequencies, transmission matrix and penetrance matrix. Helper
functions are provided to calculate the genotype frequencies and transmission
matrices for genetic models that often arise in applications. The function
genotype_probabilities calculates genotype probabilities
for a target person within a family, given the family's phenotypes.
The clipp package can handle pedigree loops, such as those
caused by inbreeding or by two sisters having children with two brothers
from an unrelated family (see (Totir et al., 2009) for a precise definition).
However, pedigrees with more than a few loops could greatly reduce the speed
of the calculation.
It is feasible to apply clipp to very large families. For instance,
in the examples for pedigree_loglikelihood,
the log-likelihood of one family with approximately 10,000 members is calculated
in less than one minute on a standard desktop computer.
Numerical issues will eventually limit the family size,
though clipp takes care to avoid arithmetic underflow and other issues.
Author(s)
Maintainer: James Dowty jgdowty@gmail.com
Authors:
Kevin Wong wongck.kevin@gmail.com
References
Cannings C, Thompson E, Skolnick M. Probability functions on complex pedigrees. Advances in Applied Probability, 1978;10(1):26-61.
Elston RC, Stewart J. A general model for the genetic analysis of pedigree data. Hum Hered. 1971;21(6):523-542.
Lange K. Mathematical and Statistical Methods for Genetic Analysis (second edition). Springer, New York. 2002.
Lange K, Elston RC. Extensions to pedigree analysis I. Likehood calculations for simple and complex pedigrees. Hum Hered. 1975;25(2):95-105.
Totir LR, Fernando RL, Abraham J. An efficient algorithm to compute marginal posterior genotype probabilities for every member of a pedigree with loops. Genet Sel Evol. 2009;41(1):52.