Seurat - subsetting by genes expressed

Question

Originally- I was looking if in at least one of these genes were expressed:

test1 <- subset(myData,
                  (KLRC1 > 0) | (KIR2DL1 > 0) | 
                (KIR2DL3 > 0) | (KIR2DL4 > 0) |
                (KIR3DL1 > 0) | (KIR3DL2 > 0) | (KIR3DL3 > 0), slot = "data")

Now- I would like to subset if expressed in at least two of these genes- is this possible with the subset function?

Answer 1

With a little bit of workaround:

i) Add a new column to the data slot (only because your original subset() call does so but it can be raw counts or any other data matrix in your Seurat object). rowSums() determines how many non-zero counts you have.

df$non_zero <- rowSums(cbind(df$gene1 > 0, df$gene2 > 0, df$gene3 > 0, ...)) > 1

Change df with the your data slot, should be sth like YourSeuratObject@...$data.

ii) Subset the newly modified data slot, basically treating the new column as another gene. Be careful not to use this column in preprocessing steps like normalization.

YourSeuratObject <- subset(YourSeuratObject, non_zero > 1), slot = "data")