Running IKAP on fully processed Seurat project

[abedkurdi]

Hello guys,
your tool is such a great tool. I would like to ask one question: I have applied IKAP on a Seurat object that was fully processed and filtered. what I mean by filtered is that I removed empty drops and removed doublets. Is it OK to apply IKAP on this final Seurat object? I did try to run it and it worked well, but I want to make sure I am using the tool in the correct way.

Thank you very much indeed!

[abedkurdi]

I got the answer by myself: all I have to do is to set scale.data = FALSE, find.var.features = FALSE, as I have already scaled and found variable genes.

[abedkurdi]

Just to make sure I am not doing anything wrong: if I have already scaled the data, I use scale.data = FALSE, am I right?
What about if I am working on integrated data? I merged the data with normalized counts, so either I have to scale the data myself using Seurat and then call IKAP using scale.data = FALSE or I let IKAP scale the data using scale.data = TRUE, am I right?

Thanks in advance.