Exploring Diallelic Genetic Markers: The HardyWeinberg Package

Testing genetic markers for Hardy-Weinberg equilibrium is an important issue in genetic association studies. The HardyWeinberg package offers the classical autosomal tests for equilibrium, functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Recently, specific frequentist and Bayesian tests for X-chromosomal markers have been developed and included in the package. Functions for testing equilibrium in the presence of missing data by using multiple imputation are provided. The package also supplies various graphical tools such as ternary plots with acceptance regions, log-ratio plots and Q-Q plots for exploring the equilibrium status of a large set of diallelic markers. Classical tests for equilibrium and graphical representations for diallelic marker data are reviewed. Several data sets illustrate the use of the package.