How to find the standard error when the GWAS summary data does not provide?
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2 days ago

I would like to perform Two sample mendelian randomization (MR) in the MRBase platform. The platform required standard error of the SNP in the GWAS summary data to perform MR. However, the GWAS summary data that I would like to use is missing the standard error information. May I know how can I find the standard error? Thanks in advance. Attached is part of the summary data.

GWAS SE • 107 views
0
Entering edit mode
2 days ago
Lemire ▴ 610

In R, assuming the tests are two-tailed:

> BETA<- 1.947
> PValue<- 1.58e-8
>
> SE<- abs(BETA)/qnorm(1-PValue/2 )
> SE
[1] 0.3444407


Checking:

> Z<- BETA/SE
> 2*pnorm( Z, lower=F )
[1] 1.58e-08