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Correct grouped ENFC implementation #23

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rbpatt2019 opened this issue Jan 25, 2022 · 1 comment
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Correct grouped ENFC implementation #23

rbpatt2019 opened this issue Jan 25, 2022 · 1 comment
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The currently implementation of ENFC for lipid classes is not consistent with past manuscripts.
Rather than finding the mean and st.dev of the ENFC for all lipids withing the class,
we should sum the expression level of all lipids,
then calculate ENFC on those summed values.
@rbpatt2019 rbpatt2019 added the bug Something isn't working label Jan 25, 2022
@rbpatt2019 rbpatt2019 self-assigned this Jan 25, 2022
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The quickest way to implement this is to simply call a groupby().sum()
after ENFC has been calculated on the individual lipids.
This should have no downstream effects,
as A/B/U/N lipids don't use the filtered values.

Looking through the code, though,
I'm thinking a refactor might be necessary.
How everything fits together at the moment feels -
well, clunky.

@rbpatt2019 rbpatt2019 mentioned this issue Jan 25, 2022
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rbpatt2019 added a commit that referenced this issue Jan 25, 2022
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fix(pipeline.py): correct enfc implementation
73667c9 
ENFC for lipid classes is now calculated on the summed total of all lipids in that class.

BREAKING CHANGE: Prior implementations had calculated the ENFC for class by taking the mean and st.dev of the individual lipid ENFC for all lipids in a class. While not incorrect, this was inconsistent with prior work of this framework. Closes #23.
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