Subset cells by ADT expression
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Entering edit mode
3.4 years ago
chi.delta ▴ 40

Hey,

I am using the subset function if I want to make an object with e.g cells that express a specific gene as follows:

subset(x = pbmc, subset = Klrk1> 1)

However I would like to subst based the expression of an ADT marker so whenever I try the following I get an error.

NKG2Dprot<-subset(x = seu_fin, subset = NKG2D-TotalSeqC > 1) 
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells,  : 
  None of the requested variables were found: 

I also tried the same with quotes ("NKG2D-TotalSeqC") but I got the same error

Is there a way to subset my cells according to ADT markers?

Thanks a lot

10x adt seurat • 1.2k views
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Entering edit mode

Did you set the default assay to ADT before subsetting? DefaultAssay(seu_fin) <- "ADT". Otherwise you can use the assay = flag in subset.

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Yeah I have tried that one but still didnt work...

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