[R] Allelic Differentiation, sampling, unique(), duplicated()

[Philip Rhoades]

Hi people,

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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