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immunogenomics / symphony

Efficient and precise single-cell reference atlas mapping with Symphony
GNU General Public License v3.0
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argument confidence in knnPredict.Seurat #19

Closed klaramagdalena closed 2 years ago

klaramagdalena commented 2 years ago

Hi, thanks for the really nice tool!

I am running the seurat adjusted workflow and wanted saw that the argument 'confidence = TRUE' does not work for the knnPredict.Seurat() function.

Does anyone now another way of getting to this information? Thanks a lot!

Best, Klara

joycekang commented 2 years ago

Hi Klara,

Sorry that we haven't implemented this in the Seurat function yet -

If you want a workaround, we use the class:knn function for prediction under the hood (see code here), and get the prediction confidence scores from setting prob = TRUE. You could do the same, just making sure to use the harmonyPCs as the predictors for k-NN. Also note that that particular function is stochastic when there are ties, so you should set a seed.

Joyce

klaramagdalena commented 2 years ago

Hi Joyce,

thanks a lot, it worked! :)

Klara