How do I access inflection points in Seurat object?
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3.0 years ago
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I ran the following code below to calculate inflection points for the UMI counts for my single cell data using Seurat.

seurat_obj <- CalculateBarcodeInflections(seurat_obj,barcode.column = "nCount_RNA",group.column = "orig.ident",threshold.low = NULL,threshold.high = NULL)

I want to obtain the inflection points so I can create my own ggplot. I know they provide a function to create a plot but I'd rather create my own for styling purposes. I tried the code below which is provided in the documentation.

seurat_obj@tools$CalculateBarcodeInflections$inflection_points

However, this only provides me a version of the metadata and a column for the ranking of the UMI. I want the actual inflection points. Does anyone know how to extract these from the Seurat object? Or do I have to manually identify them using the cells_pass item in the list? Seems kind of a pain.

Seurat scRNA-seq • 605 views
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