Make the covariate calculation part of RF about variantspark HOT 3 CLOSED

Hi @lm-fsng what do you think about the spec above. In particular how would you see getting the importances of the covariates back (and is this even necessary)

from variantspark.

Hi @lm-fsng I have included the changes we discussed. Please confirm that you are happy with the current spec.
And also please follow up with Rob on whether the covariates need to be included in p-value caluclation.

from variantspark.

Hi @piotrszul and @rocreguant , just spoke to Rob about the covariates and the p-value calculation. He said that the continuous covariates would be systematically biased to be more important, which would 'push' the genotypes down on the variable importance scale. This would result in less significant SNPs if we include the covariates in the p-value calculation. The workaround that is to ignore the covariates and just use the variable importance of the SNPs in the p-value method.

from variantspark.