I have some prefiltered scRNAseq count data and want to extract counts for cells belonging to a specific cluster.
The following code retrieves the counts with gene symbols by default:
cluster01 <- subset(data_integrated,idents = c("Cluster 1")) cluster01_counts <- cluster01@assays$RNA@counts
The output looks like this (column names truncated):
X1 AAAC.. AAAC.. AAAC.. A1BG 0 0 3 A1CF 0 0 0
Column X1 contains gene symbols.
Is there a way to extract ENSEMBL IDs directly instead of gene symbols?