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emmanuelparadis / pegas

Population and Evolutionary Genetics Analysis System
GNU General Public License v2.0
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Testing HWE for X-chromosomal markers #47

Open cloudred20 opened 4 years ago

cloudred20 commented 4 years ago

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 commented 4 years ago

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