HWETRIO: Hardy-Weinberg test for trio data

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

This program is written in R (www.r-project.org). The program assumes ALL offspring of the trios are affected.

The argument for the function HWETRIO() should be a vector of 10 integers. They are the number of trios of the 10 possible trio genotypes, in the following order:

(0x0-0)
(0x1-0)
(0x1-1)
(0x2-1)
(1x1-0)
(1x1-1)
(1x1-2)
(1x2-1)
(1x2-2)
(2x2-2)

Here, 0, 1, 2 are genotypes, representing the number of allele 1.

For example, suppose the counts of the above 10 trio types are 12, 26, 19, 37, 9, 36, 10, 16, 23, and 12. Then the p-value can be obtained by calling

HWETRIO(c(12, 26, 19, 37, 9, 36, 10, 16, 23, 12))

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)