As a wrapper around runPhenoScore, calculateDrugScreen can lead to unexpected behavior when:
A doubling column is specified, but there are no condition or replicate columns.
The user expects to do count filtering and normalization using the top-level PooledScreen module functions countNormalization or filterLowCounts, but does not explicitly pass a lack of count filter as a keyword argument. This leads to an unintended second count filter when runPhenoScore applies its count filters.
This PR implements a check in _calculateGrowthFactor to catch the former and improves the docstring and signature of the calculateDrugScreen function to catch the latter.
Does pushing update the documentation/run tests automatically? How do we typically do these two?
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?