Calling gene names from a list within Seurat subset function
Entering edit mode
15 months ago
cook.675 ▴ 90

I have a list of 5 cytokines here:

cyto <- c("Ccl1", "Ccl2", "Ccl3", "Ccl4", "Ccl5")

I'm trying to get the subset function in Seurat to subset based on the expression level of one of these without referring to the actual gene name in the function. For example, here is the typical way:

Sample <- subset(Data, Ccl1 > 0)

But I would like to call it from the list. I have tried these 3 methods:

Sample <- subset(Data, cyto[1] > 0)
Sample <- subset(Data, `cyto[1]` > 0)
Sample <- subset(Data, "cyto[1]" > 0)

All 3 methods return the error which is related to not recognizing the gene name:

Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells,  : 
  None of the requested variables were found:

I can't think of another method to try. Is it possible to do this?


seurat RNA-Seq • 787 views

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