how to calculate phenotypic variance explained

[carrot881216]

Hi,

I want to calculate phenotypic variance explained, but i cannot find beta value/effect value in fastlmm result, How do I get this value? Or through what calculation can we obtain the following results?

SnpWeight SnpWeightSE EffectSize Mixing Nullh2

thanks

[CarlKCarlK]

Greetings and thanks for using FaST-LMM!

We believe that the Effect Size output is the same as PVE. Effect size is:

SNPWeight^2 * "raw" test SNP variance / phenotype variance, where

• SNPWeight is the beta for the “standardized test SNP” (where "standardized" means made to have mean 0, stdev 1)
• "raw" means the original test SNP values of “0,1,2” (the count of allele 1 or 2 [it doesn’t matter])
• The phenotype’s original values are used (so, they are not, for example, changed by regressing out the covariates)

-- Carl

Carl Kadie, Ph.D. FaST-LMM & PySnpTools Team (Microsoft Research, retired) https://www.linkedin.com/in/carlk/ Join the FaST-LMM user discussion and announcement list via email (or use web sign up)