Add in accessibility for calculateDrugScreen #94
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abearab
approved these changes
Sep 18, 2024
| """ | ||
| adat = self.adata.copy() | ||
| if 'condition' not in adat.obs.columns or 'replicate' not in adat.obs.columns: | ||
| raise ValueError("The 'condition' and 'replicate' columns self.adata.") |
Collaborator
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I think there is a missing word here, right?
| For a given phenotype score, runPhenoScore implements a count filter threshold. By default this threshold changes | ||
| any guide or target whose mean count across replicates being compared is <40 to NAs. Because this can lead to | ||
| unexpected behavior when the user relies on filterLowCounts, we specify both the count_filter_threshold and |
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We can also remove filterLowCounts if it's confusing. I had it in previous versions and it's not necessary to keep it. What do you think?
| """ | ||
| adat = adata.copy() | ||
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| if 'condition' not in adat.obs.columns: |
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This works for now, thanks for adding this as a more clear error message. We may change it in future so runPhenoScore can take "condition" as an input.
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As a wrapper around
runPhenoScore,calculateDrugScreencan lead to unexpected behavior when:PooledScreenmodule functionscountNormalizationorfilterLowCounts, but does not explicitly pass a lack of count filter as a keyword argument. This leads to an unintended second count filter whenrunPhenoScoreapplies its count filters.This PR implements a check in
_calculateGrowthFactorto catch the former and improves the docstring and signature of thecalculateDrugScreenfunction to catch the latter.Does pushing update the documentation/run tests automatically? How do we typically do these two?