Perhaps a naive question, but it's just not clear to me. From the adapted FaST-LMM program EWASher I get this output.
SNP Chromosome GeneticDistance Position Pvalue Qvalue N NullLogLike AltLogLike SnpWeight SnpWeightSE OddsRatio WaldStat NullBias NullCov00Weight NullCov01Weight NullCov02Weight NullCov03Weight NullCov04Weight NullCov05Weight NullCov06Weight NullCov07Weight NullCov08Weight NullCov09Weight NullCov10Weight NullCov11Weight NullCov12Weight NullVar rs12345 5 395444 395444 1.216e-32 4.658e-27 475 -310.2 -239 -0.2938 0.02281 2.272 166 0.4021 -0.01345 -0.06752 -0.0474 0.0003574 0.0002916 0.000799 -0.0002633 0.001334 0.0003579 0.0005426 0.0003502 -0.001946 0.000124 0.2161
What are the effect size (beta), and corresponding standard error? Is that
OddsRatio? If I calculated
exp(-0.2938), I do not get
OddsRatio=2.272, conversely if I do
ln(2.272) it's not immediately clear to which column this corresponds? The model I used contained a couple of covariates, perhaps the
OddsRatio is that of the full model, and
SnpWeight is that of the model without covariates, or vice versa?
It's not immediately clear to from the paper either.
Thanks and best,