I am trying to obtain in PLINK the polygenic scores of a sample of individuals. I simulated a very simple example to see whether I could make it work, but it seems that it is not.
I have simulated data for 3000 individuals and 2 SNPs. I created a file .raw that has three columns: SNPid, Reference allele, and score. In the score column I put the log of odds ratio for significantly associated SNPs. In the reference allele column I just ranfomly set everything to "A", but I do not know whether this is correct, and possibly this is why I am getting an error afterwards. I ran the --score command in plink and I obtain a file where the "score" column is all "0".
Can anyone help?
What do I have to put for "reference allele" if my data is simulated?