Contains tools for exploring HardyWeinberg equilibrium (Hardy, 1908; Weinberg, 1908) <doi:10.1126/science.28.706.49> for bi and multiallelic genetic marker data. All classical tests (chisquare, exact, likelihoodratio and permutation tests) with biallelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the Xchromosome are included (Graffelman & Weir, 2016) <doi: 10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multiallelic variants. Special test procedures that jointly address HardyWeinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multiallelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of biallelic markers: ternary plots with acceptance regions, logratio plots and QQ plots.
Package details 


Author  Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb] 
Maintainer  Jan Graffelman <[email protected]> 
License  GPL (>= 2) 
Version  1.6.3 
URL  https://www.rproject.org http://wwweio.upc.edu/~jan 
Package repository  View on CRAN 
Installation 
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