diff --git a/sgkit/stats/regenie.py b/sgkit/stats/regenie.py index 56b7d767..c91096f4 100644 --- a/sgkit/stats/regenie.py +++ b/sgkit/stats/regenie.py @@ -262,7 +262,7 @@ def _stage_1(G: Array, X: Array, Y: Array, alphas: Optional[NDArray] = None) -> these predictions, a technique commonly referred to as stacking. For more details, see the level 0 regression model described in step 1 - of [Mbatchou et al. 2020](https://www.biorxiv.org/content/10.1101/2020.06.19.162354v2). + of [Mbatchou et al. (2021) Nat Genet](https://doi.org/10.1038/s41588-021-00870-7). """ assert G.ndim == 2 assert X.ndim == 2 @@ -799,9 +799,11 @@ def regenie( Defaults to 10 sample blocks split roughly across all possible samples or the number of samples, if that number is < 10. alphas - List of alpha values to use for regularization, by default None. + List of ridge parameter values to use for regularization, by default None. If not provided, these will be set automatically based on - datasize and apriori heritability assumptions. + datasize and apriori heritability assumptions. See the description of + level 0 ridge regressions in the Supporting Information of [1] for more + details. add_intercept Whether or not to add intercept to covariates, by default True. normalize