MapQuery scores between wt and mutant data

[mah238]

Hi all,

I am currently working on a wt vs mutant scRNA-seq dataset and I have used FindTransferAnchors() and MapQuery() functions to transfer cell type labels from wt to the mutant data.

Please could someone describe (or point me to a paper that does so) how MapQuery() works and what the prediction scores are.

Thank you and all the best,

Matt

[rharao]

As the documentation says (https://satijalab.org/seurat/reference/mapquery or ?MapQuery in your R session), the function is actually a convenient wrapper around three other functions: TransferData, IntegrateEmbeddings, and ProjectUMAP. You can see the documentation for those functions as well. I think the documentation for TransferData in particular will be helpful for you.

Please do follow up if you find that the available docs don't answer your questions.

[mah238]

Hi @rharao,

Please could you explain exactly what the prediction scores are? Are they percentages of cells 'confidently annotated'? How are they defined?

Thanks a lot!