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dmr and hdmr calls by default standardize the covars matrix, because they call fit(GammaLassoPath,...) on each column of counts, which standardizes its X (=covars) matrix upon entry by default.
This means we are needlessly repeating this Lasso.standardizeX call multiple times. See relevant part of Lasso.jl
A better solution would:
check for the keyword argument standardize in dmr/hdmr calls
standardize if requested before calling fit(GammaLassoPath,...) with standardize=false, keeping track of Xnorm
dmr
andhdmr
calls by default standardize thecovars
matrix, because they callfit(GammaLassoPath,...)
on each column of counts, which standardizes itsX
(=covars
) matrix upon entry by default.This means we are needlessly repeating this Lasso.standardizeX call multiple times. See relevant part of Lasso.jl
A better solution would:
standardize
in dmr/hdmr callsfit(GammaLassoPath,...)
withstandardize=false
, keeping track of Xnorm3.1 If returning DMRCoefs/HDMRCoefs (called with dmr/hdmr), then we only keep the coeffcients, so just multiply these in place by Xnorm
3.2 If returning DMRPaths/HDMRPaths (called with dmrpaths/hdmrpaths), then we need to modify path.coefs for each path.
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