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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.
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ax
New Member
Posts: 27
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Post by ax on Jul 6, 2020 2:28:32 GMT
Hi,
beta coefficients from eQTL are used. You could try to follow the standard SMR input format and re-run your program.
Input GWAS format should be as following SNP A1 A2 freq b se p n rs1001 A G 0.8493 0.0024 0.0055 0.6653 129850 rs1002 C G 0.03606 0.0034 0.0115 0.7659 129799
Input eQTL format could be found in the GCTA-SMR website.
Cheers, AX
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