Greetings,
We're pleased to announce the release of FaST-LMM 0.6.1
The single_snp function now returns the effect size of the SNP. EffectSize 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
To install:
pip uninstall fastlmm
pip install fastlmm
* Carl
