select_cells on RNA matrix

[yxsee]

Hi Ben, I saw that the function select_cells can be used to subset a list of cells from an IterableFragments object. Can the same be done on an IterableMatrix object?

[yxsee]

I figured out that I can select cells from a cell_list by using obj[ , cell_list]. But when cell_list contains duplicates, I receive an error message Error: In function [: "j" must not have duplicated values. Is there a way of selecting duplicate cells? I am trying to sample cells with replacement.

pbmc[["RNA"]]$counts[,c(1,1)]
Error: In function [: "j" must not have duplicated values
     ▆
  1. ├─IRkernel::main()
  2. │ └─kernel$run()
  3. │   └─IRkernel (local) handle_shell()
  4. │     └─executor$execute(msg)
  5. │       ├─base::tryCatch(...)
  6. │       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7. │       │   ├─base (local) tryCatchOne(...)
  8. │       │   │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  9. │       │   └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 10. │       │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11. │       │       └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 12. │       └─evaluate::evaluate(...)
 13. │         ├─base::withRestarts(...)
 14. │         │ └─base (local) withRestartList(expr, restarts)
 15. │         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 16. │         │   │ └─base (local) doWithOneRestart(return(expr), restart)
 17. │         │   └─base (local) withRestartList(expr, restarts[-nr])
 18. │         │     └─base (local) withOneRestart(expr, restarts[[1L]])
 19. │         │       └─base (local) doWithOneRestart(return(expr), restart)
 20. │         ├─evaluate:::with_handlers(...)
 21. │         │ ├─base::eval(call)
 22. │         │ │ └─base::eval(call)
 23. │         │ └─base::withCallingHandlers(...)
 24. │         ├─base::withVisible(eval(expr, envir))
 25. │         └─base::eval(expr, envir)
 26. │           └─base::eval(expr, envir)
 27. ├─pbmc[["RNA"]]$counts[, c(1, 1)]
 28. └─pbmc[["RNA"]]$counts[, c(1, 1)]
 29.   └─BPCells:::selection_index(j, ncol(x), colnames(x))

[immanuelazn]

Hi @yxsee , just noticed I didn't reply to this. We don't support this but this isn't fundamentally hard to implement. I'll add it on the backburner!