From fabe94823aadbfef6999bf20bada8db9c591ea84 Mon Sep 17 00:00:00 2001
From: josschavezf <joselynchavezf@gmail.com>
Date: Wed, 18 Oct 2023 14:31:45 -0400
Subject: [PATCH] fix normalization step for HDF5

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

diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R
index ca7fbba81..4840ec9eb 100644
--- a/R/auxiliary_giotto.R
+++ b/R/auxiliary_giotto.R
@@ -40,8 +40,8 @@ libNorm_giotto = function(mymatrix, scalefactor){
 #' @keywords internal
 logNorm_giotto = function(mymatrix, base, offset) {
 
-  if(methods::is(mymatrix, 'HDF5Matrix')) {
-    mymatrix@x = log(mymatrix + offset)/log(base)
+  if(methods::is(mymatrix, 'DelayedArray')) {
+    mymatrix = log(mymatrix + offset)/log(base)
     # } else if(methods::is(mymatrix, 'DelayedMatrix')) {
     #   mymatrix = log(mymatrix + offset)/log(base)
   } else if(methods::is(mymatrix, 'dgCMatrix')) {