I have made some progress trying to work out how to solve this problem but I have got a bit stuck - sorry if this turns out to be a simple exercise . .
Allelic Differentiation (AD) in genetics measures the number of different alleles between (say) two populations eg:
Organisms in Pop 1 have alleles: a, b, c, d, e
Organisms in Pop 2 have alleles: b, b, c, d, e
Different (unique) alleles (n) are: a
[unique() does not do what I want here for comparing these two vectors and I can't get combinations of unique() and duplicated() to work either.]
Total alleles = 10
Therefore AD = (2 * n) / 10 = 0.2
What I want to do is compare two populations of 200 organisms each but sampling for only 20 at a time.
So there are 200!/((200-20)! * 20!) possible combinations of samples in each population.
For all possible combinations of sample pop1 and sample pop2 I want to measure AD ie (200!/((200-20)! * 20!) * 200!/((200-20)! * 20!) ) calculations.
As well as the unique allele problem, can someone suggest how I can do the sampling loops?
Thanks,
Phil. -- Philip Rhoades
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