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uqrmaie1 / admixtools

https://uqrmaie1.github.io/admixtools
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The order of pops in outgroup f3 test #54

Closed hungweichen0327 closed 12 months ago

hungweichen0327 commented 1 year ago

Dear @uqrmaie1,

I would like to confirm the order of 3 pops when running outgroup f3 statistics by qp3pop. As I know, Admixtools2 computes 𝑓3 statistics of the form 𝑓3(𝐴;𝐵,𝐶) and I would use qp3pop(f2_blocks, pop1, pop2, pop3) to do 𝑓3 statistics. I want to confirm the order of the pops.

In 𝑓3(𝐴;𝐵,𝐶): pop1 refer to A pop2 refer to B pop3 refer to C

So I should put outgroup in pop1. Is that correct?

Thank you for the help!

uqrmaie1 commented 1 year ago

Yes, that's correct. In the original qp3Pop, to get 𝑓3(𝐴;𝐵,𝐶), you would specify the populations in the order B, C, A (source 1, source 2, target), but in Admixtools2, it is A, B, C (target, source 1, source 2).

hungweichen0327 commented 12 months ago

Dear @uqrmaie1, Thank you for the kind reply. I got it!