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Question: appending information to seurat object meta.data
1
gravatar for cook.675
12 months ago by
cook.675 • 40
cook.675 • 40 wrote:

I have a seurat object called AllCells.combined, and I wish to identify within the object all the cells that have expression of gene "Ighm" > 0; and also identify all cells that have expression of "Ighm" = 0

An easy way to do this would be to append it to the meta.data but I can't quite get it.

I tried:

AllCells.combined$IGHMPOS <- WhichCells(AllCells.combined, expression = Ighm > 0)

and got this error: Error: Cannot add more or fewer cell meta.data information without values being named with cell names

I then tried this:

AllCells.combined$IGHMPOS <- AllCells.combined["Ighm" > 0, ]

and got this error:

Error in [.Seurat(AllCells.combined, "Ighm" > 0, )Incorrect number of logical values provided to subset features`

I know its something simple Im missing

Thanks in advance!
seurat scrna • 1.9k views
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modified 5 months ago by atakanekiz • 250 • written 12 months ago by cook.675 • 40
0
gravatar for atakanekiz
5 months ago by
atakanekiz • 250
atakanekiz • 250 wrote:

Try using an ifelse approach.

poscells <- WhichCells(AllCells.combined, expression = Ighm > 0)

AllCells.combined$IGHM_status <- ifelse(colnames(AllCells.combined) %in% poscells, "IGHM_POS", "IGHM_NEG))
ADD COMMENT • link written 5 months ago by atakanekiz • 250
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