I have 3 replicate samples from a scRNA seq experiment; call them V1, V2, V3. I merged them into one large object "Object". When I merged them I appended the replicate name to the column barcodes, for example V2_ATGGAGTGGAT etc...
Object has a meta data column for cell cycle state located at
Object$"Phase" . These are either "G1", "G2M", or "S;
The Object also has cluster information that is located at
What I want to do is; for each replicate sum the number of cells in cluster x that are in cell phase "y"
So for example: For V1, sum the number of cells in G1 that are in cluster 1. Then I will repeat this for all clusters and cell phases and replicates to plot some data.
I can get the cluster and phase cell sum here:
V.G1 <- sum(Object$"Phase" == "G1" & Object$"seurat_clusters" == 0)
But its not clear how to specify the replicate identifier for this operation?