[adegenet-forum] Significance of allelic contribution to discriminant functions

[Caitlin Collins]

Hi Charlie,

Good question. Technically, there is no one "correct" statistical solution
to your problem. But, there *are *a number of ways of approaching the
problem with more statistical rigour than simply using an arbitrary
threshold as you have done.

Have you taken a look at the snpzip function in the adegenet packge? If
not, just type "?snpzip" into R with the adegenet package loaded. With this
function, you can apply one of seven different hierarchical clustering
formulas to the allelic contributions generated by dapc. Essentially, each
hierarchical clustering method uses a unique approach to determine where
the threshold should be drawn. I should note, however, that this
descriptive approach will not have an associated p-value. You may want to
try out a few different methods before deciding which variables you want
to consider "most significant".

I hope that helps!

Best,
Caitlin
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