From 283dfededb625bb29422dc3bbaeda70da1b2c324 Mon Sep 17 00:00:00 2001
From: plger <pl.germain@gmail.com>
Date: Mon, 6 Jan 2025 15:50:25 +0100
Subject: [PATCH] makes coercion only on individual samples

---
 R/misc.R        | 4 ++--
 R/scDblFinder.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/misc.R b/R/misc.R
index 52326f1..e82bfa7 100644
--- a/R/misc.R
+++ b/R/misc.R
@@ -433,7 +433,7 @@ propHomotypic <- function(clusters){
               rank=max(dims))$x[,seq_len(max(dims))]
 }
 
-.checkSCE <- function(sce){
+.checkSCE <- function(sce, coerce=TRUE){
   msg <- paste(
     "`sce` should be a SingleCellExperiment, a SummarizedExperiment, ",
     "or an array (i.e. matrix, sparse matric, etc.) of counts.")
@@ -446,7 +446,7 @@ propHomotypic <- function(clusters){
   }
   if( !("counts" %in% assayNames(sce)) )
     stop("`sce` should have an assay named 'counts'")
-  if(!is(counts(sce),"DelayedMatrix"))
+  if(coerce || !is(counts(sce),"DelayedMatrix"))
     counts(sce) <- as(counts(sce),"CsparseMatrix")
   if(any(counts(sce)<0))
     stop(msg, "\n", "The data contains negative counts!")
diff --git a/R/scDblFinder.R b/R/scDblFinder.R
index f77e35a..d14ce22 100644
--- a/R/scDblFinder.R
+++ b/R/scDblFinder.R
@@ -217,7 +217,7 @@ scDblFinder <- function(
          " works if `sce` is a SingleCellExperiment.\n",
          "Please pass the vector of labels.")
   }
-  sce <- .checkSCE(sce)
+  sce <- .checkSCE(sce, coerce=is.null(samples))
   score <- match.arg(score)
   knownUse <- match.arg(knownUse)
   if(!is.null(clustCor)){