I am thinking of applying MTCOJO to do conditional analysis to some summary stats data that I have. This might be a simple question but from reading papers/documentation out there I could not immediately find the answer. I have three traits, A B and C, and want to condition on the effect of C.
When running the analysis, what is the correct way to run MTCOJO?
Should I run it for A+C ->AC and then B+C ->BC and then LDSC of the two resulting files AC and BC?
Or is it enough to do the conditioning on one file? A+C -> AC and then do LDSC with AC and B?