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name ridge parameter
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jdstamp committed Jan 29, 2024
1 parent 422d393 commit 0a5a549
Showing 1 changed file with 5 additions and 3 deletions.
8 changes: 5 additions & 3 deletions sgkit/stats/regenie.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
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