How to find the standard error when the GWAS summary data does not provide?
1
0
Entering edit mode
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. part of the GWAS summary data

GWAS SE • 107 views
ADD COMMENT
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
ADD COMMENT

Login before adding your answer.

Traffic: 1715 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6