I am looking to calculate the frequencies of all possible combinations of a group of SNP genotypes, in a population. This would be done based on the minor allele frequencies acquired in our population data. I just have a question on whether the following is the right way to do it:
If for example, we have three SNPs, their alleles, and their minor allele frequencies, with A2 being the minor allele:
SNP A1 A2 MAF SNPA A T 0.1 SNPB C G 0.3 SNPC A G 0.4
And I now have compiled the possible genotype combinations from the three SNPs:
AA-CC-AA AA-CC-AG AA-CG-AA AA-CG-AG ...
and so on for 27 combinations.
In order to calculate the frequencies of each ‘profile’, would I simply multiply all the allele frequencies? For example, the first AA-CC-AA frequency would be:
(0.9)(0.9) x (0.7)(0.7) x (0.6)(0.6)
While for the AA-CC-AG combination it would be:
(0.9)(0.9) x (0.7)(0.7) x (0.6)(0.4)
Would this be correct?
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