Statistics, Department of

The R Journal
Date of this Version
12-2017
Document Type
Article
Citation
The R Journal (December 2017) 9(2); Editor: Roger Bivand
Abstract
The alleHap package is designed for imputing genetic missing data and reconstruct non recombinant haplotypes from pedigree databases in a deterministic way. When genotypes of related individuals are available in a number of linked genetic markers, the program starts by identifying haplotypes compatible with the observed genotypes in those markers without missing values. If haplotypes are identified in parents or offspring, missing alleles can be imputed in subjects containing missing values. Several scenarios are analyzed: family completely genotyped, children partially genotyped and parents completely genotyped, children fully genotyped and parents containing entirely or partially missing genotypes, and founders and their offspring both only partially genotyped. The alleHap package also has a function to simulate pedigrees including all these scenarios. This article describes in detail how our package works for the desired applications, including illustrated explanations and easily reproducible examples.
Included in
Numerical Analysis and Scientific Computing Commons, Programming Languages and Compilers Commons
Comments
Copyright 2017, The R Foundation. Open access material. License: CC BY 4.0