Question: Calling gene names from a list within Seurat subset function
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gravatar for cook.675
9 months ago by
cook.67560
cook.67560 wrote:

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?

Thanks!

rna-seq seurat • 437 views
ADD COMMENTlink written 9 months ago by cook.67560
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