How is PLINK obtaining p-values and coefficients for linear regression

Question

[sakura]

I'm a beginner in PLINK, and I'm now learning about association analysis with quantitative traits. Are the p-values and coefficient estimates in the PLINK output generated from conducting multiple "simple linear regression" across all sites, or are they obtained from conducting one "multiple linear regression" which includes genotypic information from all sites?

Answer 1

[chrchang523]

From the top of https://www.cog-genomics.org/plink/2.0/assoc#glm :

--glm is PLINK 2.0's primary association analysis command.

For quantitative phenotypes, --glm fits the linear model

y = G\beta_G + X\beta_X + e

for every variant (one at a time)

[sakura]

Thanks a lot! It was super helpful.