Beta calculation for SNPs in PLINK

Question

[fatma.mokhtar]

Hi,

How is Beta calculated in PLINK, as I have three genotypes AA, AB, and BB of one SNP and I have the average of blood pressure of each genotype?

Thank you in advance

Answer 1

[Sam]

If I remember correctly, the beta is generated via linear regression, with the genotype coded as 0, 1 and 2. If there is no covariate, then the beta is basically obtained by

Phenotype ~ Genotype