SingleR annotation of several slots/patients
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Bine ▴ 40
@bine-23912
Last seen 10 weeks ago
UK

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.

enter image description here

How can I do this?

Thank you, Bine

SingleR • 806 views
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ATpoint ★ 3.9k
@atpoint-13662
Last seen 16 hours ago
Germany

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.

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Thank you for your comment & help. When I try to run it with clusters it complains about having multiple layers:

GetAssayData(kid.filtered,clusters = Idents(kid.filtered))
   Warning: The following arguments are not used: clustersError in `GetAssayData()`:
    ! GetAssayData doesn't work for multiple layers in v5 assay.
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Ah, I just found the function JoinLayers.. I think this should help...

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