From 6ee929843f375cd3a13acc62eee5fa4f920574a7 Mon Sep 17 00:00:00 2001
From: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: Wed, 4 Jun 2025 14:05:45 +0200
Subject: [PATCH] RowSums2 requires DelayedMatrixStats if count matrix is of
 class dgCMatrix. Added DelayedMatrixStats to suggested packages in
 DESCRIPTION and implemented conditional loading of package if count matrix is
 sparse

---
 DESCRIPTION | 1 +
 NAMESPACE   | 1 +
 R/utils.R   | 9 ++++++++-
 3 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ae2cd5c..1fa4b8d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,6 +28,7 @@ Suggests:
     AUCell,
     BiocParallel,
     BiocStyle,
+    DelayedMatrixStats,
     dplyr,
     fgsea,
     GSEABase,
diff --git a/NAMESPACE b/NAMESPACE
index abc7840..51d6485 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,6 +18,7 @@ export(splitEnrichment)
 import(ggplot2)
 importFrom(MatrixGenerics,rowMeans2)
 importFrom(MatrixGenerics,rowSds)
+importFrom(MatrixGenerics,rowSums2)
 importFrom(SummarizedExperiment,colData)
 importFrom(ggdist,stat_pointinterval)
 importFrom(grDevices,hcl.pals)
diff --git a/R/utils.R b/R/utils.R
index 793217c..483674c 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -150,6 +150,7 @@
 # -----------------------------------------------------------------------------
 #  EXPRESSION MATRIX EXTRACTOR -------------------------------------------------
 # -----------------------------------------------------------------------------
+#' @importFrom MatrixGenerics rowSums2
 .cntEval <- function(obj, assay = "RNA", type = "counts") {
   if (.is_seurat(obj)) {
     # Use generic accessor if available
@@ -177,10 +178,16 @@
   } else {
     cnts <- obj
   }
+  # Conditionally require DelayedMatrixStats if cnts is dgCMatrix
+  if (inherits(cnts, "dgCMatrix")) {
+    if (!requireNamespace("DelayedMatrixStats", quietly = TRUE)) {
+      stop("Package 'DelayedMatrixStats' is required to handle sparse matrices. Please install it with BiocManager::install('DelayedMatrixStats').")
+    }
+    loadNamespace("DelayedMatrixStats")
+  }
   cnts[MatrixGenerics::rowSums2(cnts) != 0, , drop = FALSE]
 }
 
-
 # -----------------------------------------------------------------------------
 #  ATTACH / PULL ENRICHMENT MATRICES ------------------------------------------
 # -----------------------------------------------------------------------------