Good morning everyone,

I have just started working with the SingleR package for annotation of my single cell clusters and was wondering the following:

So far I have only done the annotation for one patient via

#Annotate by patient 
pbmc_counts_1 <- GetAssayData(kid.filtered, slot = 'counts.Patient_1')


pred <- SingleR(test = pbmc_counts_1,
        ref = ref,
        labels = ref$label.main)

However, now I have combined several patients into one Seurat object and I would like to annotate them at the same time.

How can I do this?

Thank you, Bine

SingleR is agnostic. It does not know "patients" or "groups". You can either annotate each cell individually and then map this back to your patients, or use the clusters argument to do this per "cluster". Here, cluster can be anything. A patient, group, clusters within patients or across patients, any subset of cells that you define. You have full flexibility, choice is yours. You probably want to read https://bioconductor.org/books/3.17/SingleRBook/ as well.