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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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Force assignment to all cells? #57

Closed igrabski closed 2 years ago

igrabski commented 3 years ago

Hi all,

I have a question about classifying cells -- is it possible to turn off the functionality to flag some cells as "unassigned," or in other words, to force all cells to be assigned a cell-type label? I see that the sensitivity with which a cell is marked unassigned can be toggled through the rank_prob_ratio parameter, but it seems that this parameter must always be greater than 1, whereas all cells would only be forced to be assigned a label if this parameter were equal to 1 (if I understand it correctly). Please let me know!

Thanks so much.

hpliner commented 2 years ago

Hello, Apologies for the delay. Unfortunately, at this time there isn't a way to do this - the idea being that if the rank_prob_ratio was equal to 1, then there would be multiple cell types that were equally likely to be assigned.

hpliner commented 2 years ago

I'm going to go ahead an close, reopen if you have further issues