Question: convert GWAS Zscore back to OR
gravatar for Andy
4.1 years ago by
Andy0 wrote:

HI, I have got a GWAS summary data with Z-socres and P-values for each SNP, I know that z = logor / seor I am wondering if it is possible to convert Z-scores back to OR values. Thank you!

snp • 3.7k views
ADD COMMENTlink modified 4.1 years ago by tpoterba50 • written 4.1 years ago by Andy0
gravatar for tpoterba
4.1 years ago by
tpoterba50 wrote:

You need the OR standard error to do that. Z-scores and p-values only describe your confidence that your estimated odds ratio isn't actually coming from the null. Your p-value is roughly a function of your power to detect a SNP and the effect of that SNP.

If all I know is that I have a p-value of 1e-9, then it's possible that this p-value came from a SNP with a big effect in a small cohort (low power and high effect), or a large effect SNP in a large cohort (high power and low effect). I can't distinguish these two without more information.

ADD COMMENTlink written 4.1 years ago by tpoterba50

Many thanks to your detailed answer!

Z score is often mentioned in GWAS but in fact I am not sure about its defination. You say that "Z-scores and p-values only describe your confidence" Did this mean that Z-score in GWAS is just like z-score being the statistics to normal distribution. How is it associated with z = logor / seor?

ADD REPLYlink written 4.0 years ago by Andy0

Hi! Did you find answer to your question? I'm trying to understand it as well.

ADD REPLYlink written 2.7 years ago by nomadkml0
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