Units for effect size

[Nicolas Alexandre]

Hello,

I am trying to determine what the units are for beta values in the association test output files. I know from previous discussions that there may be some internal standardization of phenotypes in GEMMA, but I am unsure whether these beta values are units measured per additional allele (millimeters for example) or in standard deviations per additional allele.

Thank you,

Nicolas

[Xiang Zhou]

The units are based on the genotypes provided in the input genotype file. Specifically, if the genotype file contains original genotype coded as 0/1/2, then beta values are units measured per additional allele. If the gneotype file contains standardized genotype, then beta values are units for standard deviations per additional allele.