HWECC: Hardy-Weinberg test for case-control data

URL of this page: http://biostat.mc.vanderbilt.edu/HWECC

This program is written in R (www.r-project.org). The main function is HWECC(), which uses three other internal functions fun1(), fun2(), and fun3().

For example, for a SNP with case genotype counts 61, 48, 23 and control genotype counts 98, 77, 9, if the disease prevalence is 0.06, the p-value is obtained by calling

HWECC(prev=0.06, case=c(61,48,23), control=c(98,77,9))

The paper that describes the method is:

Li M, Li C (2008) Assessing departure from Hardy-Weinberg equilibrium in the presence of disease association. Genetic Epidemiology 32:589-599 (PMID: 18449919) (paper)