I am running conditional analysis using the COJO module.
I wanted to ask about the p-value threshold (--cojo-p flag): my input file contains GC-corrected p-values although BETAs and SEs come from the original association testing. So, there is a "mismatch" between BETAs/SEs and p-values. Is this a problem? Are the BETAs and SEs being combined in any way with the p-values in GCTA's computations?
Thank you, Mushashi
Last Edit: Apr 10, 2019 17:08:03 GMT by mushashi21