I have a list of 700 snps and the associated genotypes for 8500 individuals. I am trying to analyze the association between the SNPs and two quantitative traits. ( => which snp is associated the most with each one of them).
I was considering to generate a linear regression model with each of the quantitative traits as Y variables, adjust by age and sex and then plot the log distribution of p values. (pvals for QT1) versus pvals for QT2).
regression QT1 : QT2, age, sex regression QT2: QT1, age, sex
Is there a better approach/method/software tool in performing this type of analysis?
Thanks in advance.
I have tried using plink for this , --assoc option , but I have only got the basic snp-qt association results. I have probably done something wrong when using --gxe returned only NA values...although I think I have used the correct input formats ..