From 25da3de3dff51ac2eed7619fcd5aa93bb1787aa5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Trimbour?=
 <77151348+r-trimbour@users.noreply.github.com>
Date: Fri, 21 Jun 2024 13:28:10 +0200
Subject: [PATCH] Update GENIE3 to use assays slot of hummus_objects

---
 R/layers.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/layers.R b/R/layers.R
index a49dffa..a8fc1e1 100644
--- a/R/layers.R
+++ b/R/layers.R
@@ -181,7 +181,7 @@ compute_gene_network <- function(
             verbose = verbose)
 
     # infer network
-    weightMat <- GENIE3::GENIE3(as.matrix(hummus[[gene_assay]]@counts),
+    weightMat <- GENIE3::GENIE3(as.matrix(hummus@assays[[gene_assay]]@counts),
                                regulators = tfs,
                                nCores = number_cores)
     # get edge list