Many R Flow Cytometry pakages perform clustering or data analysis based on cell identification.

For example, cytoMEM require a cluster ID for each cell to compute marker expression for the cell cluster.

I did write the following r code to annotate a matrix but it has several drawbacks:

• It is cumbersome to make many clusters (ex: lymphocytes, monocytes, granulocytes...)
• It relies on a 2 dimensions graph (CD45 vs SS in my example) but depending on the scientific question, I might need different gating strategies
• Some cells are not clustered because they fall out of the different gates that I did define
• I need additionnal code to add the markers names to the output matrix

library(flowCore)
library(CytoExploreR)
library(purrr) 

frame <- read.FCS("myFcsFile.fcs")
cell_gate <- cyto_gate_draw(frame,
                            parent = "root",
                            alias = "lymphocytes",
                            channels = c("FL10-A", "SS-A"),
                            axes_limits="machine",
                            title ="select lymphocytes")
  cell_filter <-filter(frame, cell_gate[[lymphocytes]])
  vec <- cell_filter@subSet

mat <- exprs(frame)
mat <- list(mat)
annotated_cells <- cbind, c(mat, vec)

So my question is the following: What method or package do you use to manually define cell population clusters for further analysis?

Is there an easy and flexible method to do such annotation of a fcs file?

The output should be a matrix rather than a fcs file as it is more widely usable in R.

Thank you for any help.