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HWEBayes, swapping the homozygotes genotype frequencies

2 messages · stat999, Aaron Mackey

#
I evaluated the Bayes factor in the k=2 allele case with a "triangular" 
prior under the null as in the example in the help file:


HWETriangBF2(nvec=c(88,10,2)) 
[1] 0.4580336

When I swap the n11 entry and n22 entry of nvec, I received totally
different Bayes factor:
[1] 5.710153
In my understanding, defining the genotype frequency as n11 or n22 are
arbitrary.
So I was expecting the same value of Bayes factor.

This is the case for conjugate Dirichlet prior:
c(1,1,1))
[1] 1.542047
c(1,1,1))
[1] 1.542047

Could you explain why the HWETriangBF2 is returining completely different
values of Bayes Factor??


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