From 4e59e2d02b5a4711f5b39769119799842a2e4e72 Mon Sep 17 00:00:00 2001
From: nickhir <nick.hirschmueller@yahoo.de>
Date: Wed, 12 Apr 2023 17:51:31 +0200
Subject: [PATCH] fixed bug where CompCCAT would fail if exp.m is of class
 dgeMatrix

---
 R/CompCCAT.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/CompCCAT.R b/R/CompCCAT.R
index d371864..545febd 100644
--- a/R/CompCCAT.R
+++ b/R/CompCCAT.R
@@ -69,8 +69,10 @@ CompCCAT <- function(exp.m, ppiA.m){
 
     if(classMATRIX=="matrix"){ ## ordinary matrix
       ccat.v <- as.vector(cor(exp.m[match(commonEID.v,rownames(exp.m)),],k.v));
-    }
-    else if (classMATRIX=="dgCMatrix"){
+    } else if (classMATRIX=="dgeMatrix"){ # ordinary dense matrix in S4 Matrix representation. 
+      exp.m <- as.matrix(exp.m) # dense S4 matrix representation to base matrix presentation
+      ccat.v <- as.vector(cor(exp.m[match(commonEID.v,rownames(exp.m)),],k.v))
+    } else if (classMATRIX=="dgCMatrix"){
       ccat.v <- as.vector(corSparse(exp.m[match(commonEID.v,rownames(exp.m)),],Matrix(matrix(k.v,ncol=1))));
     }