ENH set reference level in DeseqDataSet#109
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| ref_level=["group", "Y"], | ||
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| assert "group_X_vs_Y" in dds.obsm["design_matrix"].columns |
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do you think it might be worth for checking if it is correct? I still accept and leave the decision to you
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You mean checking whether the column contains correct data? It's true that this only checks that it exists.
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Yes, that's what I was thinking about. Would it be difficult to add?
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What does your PR implement? Be specific.
This PR allows users to set the desired reference (control) level when creating a
DeseqDataSet, instead of only the tested level as previously.This ensures that users have control over the LFC coefficients created by a
DeseqDataSet, so that they can ensure that the relevant coefficients exist when applyinglfc_shrink, which wasn't the case when only the tested level could be set.