Possible to only return Lymphocyte (or Myeloid labels), not both?

[s2hui]

Hello,

I have an input data set that contains only Lymphocytes. When I look at the immclassifier predicted labels they contain a mixture of Myeloid and Lymphocyte labels. Because I have manually labelled my data set, I know there should not be any Myeloid labels.

I am wondering if it is possible to turn off the Myeloid label predictions? Or if I can somehow filter the prediction prob file that is output at the end to disregard the Myeloid labels?

Thank you,

[xliu-uth]

Hi,
This is a great question.
What's the percentage of cells predicted to be myeloid cells?
The current version of ImmClassifier doesn't support turning off the myeloid labels. I can prepare a post-processing script to parse the output file that choose the top candidate under lymphoid lineage for those cells predicted to be myeloid cells. You can also examine the probability of those cells under lymphoid lineage to process it on your own. For example, compare the probabilities of NK vs. CD4T vs. CD8T, to tell whether they are NK, CD4T or CD8T cells.