Transfer malignant/non-malignant labels from scRNA-seq to scATAC-seq

[DaianeH]

Hi, thank you again for developing this great tool.

I have a dataset of bone marrow scATAC-seq (mostly AML patients), with clusters identified through unconstrained + constrained integration with a dataset of scRNA-seq generated from the same patients. We are now in the process of identifying malignant and non-malignant cells in the scRNA-seq data. Once that is done, I would like to transfer these labels - malignant/non-malignant - to the scATAC-seq data. I can see how to do that via unconstrained integration, by setting the parameter groupRNA with the name of the scRNA-seq metadata column isMalignant. However, is there a way to additionally apply constrained integration?

Thank you so much in advance,