mhkowalski
commented
1 year ago Hi,
You can use something like this
> length(WhichCells(obj, expression = Klf1 > 0))
[1] 515
> t = "Klf1"
> sum(GetAssayData(obj, slot="data", assay="RNA")[t,]>0)
[1] 515
#to get barcodes
length(Cells(obj)[GetAssayData(obj, slot="data", assay="RNA")[t,]>0])
[1] 515
Hello,
I am trying to subset cells that are expressing any pairs of genetic markers that are from two distinct macro-types of cells.
I have for different cellular macro-types a list of corresponding genetic markers that identify the macro-types. What I want is to exclude all cells that express markers identifying two or more distinct macro-types.
I wanted to use WhichCells() to subset these cells, as I have the names of the markers in a list which I can access in the following way:
str(markers.nathans)markers.nathans[[1]][1]With the following output:
List of 11$ amacrine_cells : chr [1:8] "Gad1" "Slc6a9" "Stx1b" "Calb2" ...$ astrocytes : chr [1:4] "Pax2" "Gfap" "Vim" "Glul"$ cone_bipolar_cells : chr [1:9] "Scgn" "Grik1" "Vsx1" "Lhx4" ...$ cones : chr [1:5] "Opn1sw" "Opn1mw" "Gnat2" "Arr3" ...$ horizontal_cells : chr [1:4] "Lhx1" "Calb1" "Gja10" "Onecut1"$ muller_glia : chr [1:9] "Slc1a3" "Apoe" "Dkk3" "Gpr37" ...$ perivascular_cells : chr [1:6] "Myl9" "Cspg4" "Pdgfrb" "Myh11" ...$ retinal_ganglion_cells : chr [1:4] "Sncg" "Pou4f1" "Nrn1" "Slc17a6"$ rod_bipolar_cells : chr [1:7] "Trpm1" "Grm6" "Sebox" "Prkca" ...$ rods : chr [1:5] "Rho" "Gnat1" "Cnga1" "Nrl" ...$ vascular_endothelial_cells: chr [1:8] "Cldn5" "Cdh5" "Pecam1" "Vwf" ...'Gad1'However, the following command:
length(WhichCells(rfull.combined, expression = markers.nathans[[1]][1] > 0, slot = 'counts'))returnsError in FetchData.Seurat(object = object, vars = unique(x = expr.char[vars.use]), : None of the requested variables were found:As, the same command with the marker's name written directly without quotes,
length(WhichCells(rfull.combined, expression = Gad1 > 0, slot = 'counts'))correctly returns the number of cells expressing Gad12371I tried a couple things hoping to match the expected format for expression = in WhichCells(), but without any luck so far. Is there any way to make this work ?
I have a workaround that is quite lengthy:
length( rfull.combined@assays$RNA@data[ rownames(rfull.combined@assays$RNA@data) == markers.nathans[[1]][1],rfull.combined@assays$RNA@data[rownames(rfull.combined@assays$RNA@data) == markers.nathans[[1]][1],] > 0 ] )I would really prefer to solve the previous instead of using the ugly line above ... Thank you in advance for any help or advice you can provide.