Guys, I'm running logistic regressions with plink. From the current output, I can tell the total number of individuals (case+control) from the NMISS column. My questions is, is there a way to get the number of cases and controls for each SNP as well? For example, with SNP123456, I currently know the sample size is 5,000. What's the easiest way to tell how many cases and how many controls within the 5,000 people? Greatly appreciate your help! Charlie
P.S. we dropped some genotype calls due to bad quality and we don't plan to impute the missing calls. Therefore, each SNP may have a different number of cases and controls.