Testing HWE for X-chromosomal markers

[cloudred20]

Hi,
Can the "hw.test" function of "pegas" package be used for testing HWE for X-chromosomal markers, similar to "HWChisq" of "HardyWeinberg" package? If yes, then how to input the data for males?

[emmanuelparadis]

Hi Megha,

Very good question! AFAIK, hw.test cannot analyse X-linked loci because the formula used in this function assumes all individuals are diploid. If there is another package that implements HWE-test for X-linked loci, I suggest you go ahead with it. I'll have a look at this issue for a future release of pegas -- or if someone has an idea/code to implement it.
Best, Emmanuel