Open novnex-cmd opened 3 years ago
Hi Minglong, Thank you for using MR-JTI!
The first line "expression ... " represents the effect of the expression on the trait. Correct.
So does the second line “ldsc..." represents the heterogeneity estimates? The second line represents the effect of the LD-score which is considered as a covariate here. The following rows (one raw one SNP with potential pleiotropy effect) show the heterogeneity estimates. i.e., any SNP showing a significant 'extra effect' would result in heterogeneity.
whether it is appropriate to include only SNPs with fdr<0.05 in GTEx for MR-JTI analysis Sure. However, it needs at least 20 independent IVs (SNPs) to have a robust estimate. Very few genes could have > 20 independent IVs. So, we suggest using all the cis SNPs.
Please let me know if you have any questions. Best, Dan
Thank you for your help.
I have one more question. you recommend providing LD Score when using MR-JTI. Should we include all GTEx SNP or pruned SNP to calculate LD score? Look forward for your help.
Many thanks.
Minglong Cai
Hi Minglong, All the SNPs should be included for LD score calculation. Please let me know if there is anything else I can help with. Dan
On Thu, Aug 19, 2021 at 8:29 AM novnex-cmd @.***> wrote:
Thank you for your help.
I have one more question. you recommend providing LD Score when using MR-JTI. Should we include all GTEx SNP or pruned SNP to calculate LD score? Look forward for your help.
Many thanks.
Minglong Cai
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Hi @egamazon @zdangm @gamazonlab
Thank you for sharing such a wonderful job. I would like to run MR-JTI analysis but I don't know how to explain the output file. The first line "expression ... " represents the effect of the expression on the trait. So does the second line “ldsc..." represents the heterogeneity estimates?
By the way, I wonder to know whether it is appropriate to include only SNPs with fdr<0.05 in GTEx for MR-JTI analysis. look forward for your help.
Many thanks.
Best regards,
Minglong Cai