I am using a post-gwas analysis tools to test genetic overlap between different traits based on summary level data, and it requires the effect size(beta) and SE.
So for summary stats that has the Z score measures, beta and SE are estimated by using the following formula that was published in a large scale study on Alzheimers.
- VP: phenotypic variance approximated to 1;
- ES: effective sample size
- pq: allele frequencies (p allele, q allele)
- Z: Z scores
The summary stats that I currently have access to does not have allele frequency information.
head of the summary stats:
> Chr Pos MarkerName EffectAllele OtherAllele Z P.value TotalSampleSize > 1 744055 rs3131000 a g -1.60 0.10 23546
Is there a way to calculate the Betas and SE without contacting the study, with just relying on the information that is currently publicly available.