Deleted:Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
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Entering edit mode
4 weeks ago
Jeyong • 0

This is the parital code of DoubletFinder.

# ---
annotations <- seurat_object@meta.data$seurat_clusters
homotypic.prop <- modelHomotypic(annotations)
nExp_poi <- round(0.015*nrow(seurat_objec@meta.data))
nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop))
# ---

I understand DoubletFinder has criteria of predicted doublet number. The number of cells in my sample is 1654. Then I use 0.015 at 3rd line of above code.

My questions are two.

  1. DoubletFinder has fixed number of doublets by the number of cells in a sample?
    • I check the 'expected doublet rate #34' answer. I wonder if the number of doublets is only decided by sample cell numbers.
  2. I understand 'homotypic.prop' is the proportion of homotypic doublet (doublet of same cell types). Then 'nExp_poi.adj' is the number of heterotypic doublet because I use '1-homotypic.prop'.
  • example)
nExp_poi = 100, nExp_poi.adj=80, total cell number=1654.

number of heterotypic doublet = 80
number of homotypic doublet = 20 (100-80)
number of singlet = 1554 (1654-100)

So I understand I can use only 1554 cells in downstream analysis. Is my understanding right?

Thanks for reading my question.

doublet DoubletFinder Seurat modelHomotypic • 144 views
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