Post by complexgenome on Jun 24, 2020 14:55:25 GMT
hi there devs, Thanks for this tool.
I'm running into weird situation. I run SMR on GWAS and eQTL data, where the results for p_smr stay consistent regardless of the p-eQTL and LD applied. For instance, if p-value of eQTL is 8.E-10 P-smr is 0.97, GWAS p-value is 0.97. Again, when P-eQTL is 5.47E-05 with GWAS p-value as 0.9, p-smr is 0.1. The results stay AS IS when changing LD threshold.
Are beta coefficients from eQTL used? or, SMR is simply scaling the P-value from GWAs summary statistics?
I conduct SMR analysis on small chromosome regions only.