MAINT reduce the number of arguments in _fit_rough_dispersions
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…y replacing ``counts`` and ``size_factors`` with ``normed counts``
BorisMuzellec
requested review from
maikia and
arthurPignetOwkin
as code owners
BorisMuzellec
changed the title
_fit_rough_dispersions_fit_rough_dispersions
maikia
approved these changes
Sep 22, 2023
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Thanks @maikia! |
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What does your PR implement? Be specific.
This PR is a minor refactoring of
DeseqDataSet._fit_rough_dispersions().Currently, this method takes both
countsandsize_factorsas arguments, only to compute normalized factors ascounts / size_factors[:, None].We now provide
normed_countsdirectly, which are already stored inself.layers["normed_counts"]when_fit_rough_dispersions()is called in the pydeseq2 pipeline.Likewise, we provide
normed_countsinstead ofcountsin_fit_moments_dispersions()to avoid performing the division again.