I read some papers about GWAS. i'm interested in genetic risk assessment based on common variants. Authors computed likelihood ratios (LRs) for each SNP as the ratio of the probability of the genotype in an affected person to that of an unaffected person. LRs for each locus were computed from each case-control study be dividing the genotype frequency in cases by the frequency in controls, weighted by the sample size of the study. Thus, for an individual with genotype g in SNP x found in i = 2 ...s studies, each of size S(i). (Reference: https://genomemedicine.biomedcentral.com/articles/10.1186/gm462) The formula is as follows:
i'm confused with genotype frequencies. F(g in cases) means F(cases | Aa )+F(cases | aa ), and F(g in controls) means F(controls | Aa )+F(controls | aa )??? if not, how to compute the F(g | cases ) and F(g in controls)?