"instrumented" do_SingleR

inst.R

do_SingleRi = function(sce=NULL, path="/home/vincent/tenx3k.h5ad", 
    ref=celldex::HumanPrimaryCellAtlasData(), 
    ref.type = "label.main",
    min.common = 1000, assay.type.test=1L, instrument=TRUE,
    clprocid=NULL, ...) {
  if (instrument == TRUE && is.null(clprocid)) stop("clprocid not set")
  cl_timestamp(clprocid, "init")
  stopifnot(ref.type %in% c("label.main", "label.fine"))
  if (is.null(sce)) {
   is_h5ad = length(grep("h5ad$", path)==1)
   is_rda = length(grep("rda$", path)==1)
   is_rds = length(grep("rds$", path)==1)
   chk = sum(c(is_h5ad, is_rda, is_rds))
   if (chk != 1) stop("path must have suffix h5ad, rda or rds")
   if (is_h5ad) sce = ingest_h5ad(path)
   else if (is_rda) sce = get(load(path))
   else if (is_rds) sce = get(readRDS(path))
   stopifnot(inherits(sce, "SingleCellExperiment"))
   }
  cl_timestamp(clprocid, "pre-singler")
  preds = SingleR(test=sce, 
    ref=ref, labels=ref[[ref.type]], assay.type.test=assay.type.test,...)
  cl_timestamp(clprocid, "post-singler")
  list(input=sce, preds=preds)
}