Fix: raise error when cooks outliers should have been refitted but were not #48
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…ed DeseqDataSet has "refit_cooks" set to True but Cooks outlier were not refitted
…ing a DeseqStats object from a DeseqDataSet object whose Cooks outliers were not refitted but should have been
pydeseq2/DeseqStats.py
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| assert hasattr(dds, "replaced"), ( | ||
| "dds has 'refit_cooks' set to True but Cooks outliers have not been " | ||
| "refitted. Please run 'dds.refit()' first or set 'dds.refit_cooks' " | ||
| "to False." | ||
| ) |
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Instead of an AssertionError, what about raising an AttributeError? Otherwise LGTM
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Good idea, an AttributeError might be more appropriate indeed
…liers were not refit but should have been
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LGTM
if in the description of the PR you use: closes #issue_number the issue will automatically be closed when the PR is merged ( there are other possible keywords: https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue )
Co-authored-by: Maria Telenczuk <[email protected]>
Thanks, I didn't know we could do that :) |
This PR addresses issue #46 by raising an
AssertionErrorif one tries to initialize aDeseqStatsobject from aDeseqDataSetwithrefit_cooks=Truebut whose outliers were not refit.This is detected by checking that the
DeseqDataSethas areplacedattribute.A corresponding pytest was also added.
Closes #46.