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[feature] Transition the phenotype associations to non-parametric tests #171

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merged 10 commits into from
Apr 15, 2024

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@cdiener cdiener commented Apr 9, 2024

Purpose

The former strategy of identifying metabolite:phenotype associations with coefficients from a LASSO models has proven to be quite unstable due to (a) the non-uniqueness of the coefficients and (b) instability across scikit-learn versions and initialization. This PR switches this to a more stringent approach that uses Mann-Whitney U or Spearman rho tests to assess metabolite-level associations. A LASSO models is still fit to assess the overall/global association with the phenotype.

Visualization

The visualization is similar but now shows a confusion matrix for binary outcomes. A quantitative effect measure will be used instead of coefficients.

example visualization

Side effects

This adds new example data sets to help test and document the new functionality.

TODO

  • update tests
  • update docs

@cdiener cdiener force-pushed the feature/new_phenotype branch 3 times, most recently from 5f050a2 to a4b2c7d Compare April 12, 2024 11:11
@cdiener cdiener merged commit 8e32825 into main Apr 15, 2024
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