2
$\begingroup$

I am trying to determine exactly what method PLINK uses for meta-analysis. I can't find it in the program documentation/FAQ anywhere. Inverse variance? (given the meta command only requires effect size and SE)? ALso, what method its using to generate a P-value?

$\endgroup$

1 Answer 1

1
$\begingroup$

the Plink method used for meta-analyses is indirectly described here:

https://www.cog-genomics.org/plink/1.9/postproc

"weighted-z' requests weighted Z-score-based p-values (as computed by the Abecasis Lab's METAL software) in addition to PLINK's usual inverse variance-based analysis. This requires P and effective sample size fields (default column names are 'P' and 'NMISS'; these can be changed with --meta-analysis-p-field and --meta-analysis-ess-field). Note that, if the numbers of cases and controls are unequal, effective sample size should be 4 / (1/<# of cases> + 1/<# of controls>)."

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.