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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

Home Page:https://www.cog-genomics.org/plink/2.0/

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covariates in plink

mfazel opened this issue · comments

commented

Hi,

This is more of a question than issue but I could not find a clear answer to it. When we use --covar flag, in the association results there are "ADD" aditive effect ("DOMDEV" if I used --genotypic as dominant deviation from additive effect) and all other "COV" variables effect that are used in the model. What I got from documentation was that "GENO_2DF" is the additive/dominant model adjusted for covariates. My question: Is "ADD" row in this file, already adjusted for covariates introduced by covar file or how can one calculate adjusted additive effect for covariates?

Thanks,
Mehdi

commented
  • The plink2-users Google group is a better place to ask (and search for answers to) usage questions.
  • The GENO_2DF row contains a joint-test p-value. The ADD row is adjusted for covariates.
commented

Thanks a bunch for clarification. Made it easier!