From 931c31bce7e74a1c2d9a7de816f6c6cdee036122 Mon Sep 17 00:00:00 2001
From: Zhisong He <zhisong.he@bsse.ethz.ch>
Date: Fri, 19 Apr 2024 10:48:04 +0200
Subject: [PATCH] Update README.md

---
 README.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 16f71fa..b7d54b4 100644
--- a/README.md
+++ b/README.md
@@ -32,23 +32,23 @@ data(motifs)
 seurat_object <- Seurat::FindVariableFeatures(seurat_object, assay='RNA')
 
 # Initiate GRN object and select candidate regions
-seurat_object <- initiate_grn(seurat_object)
+grn_object <- initiate_grn(seurat_object)
 
 # Scan candidate regions for TF binding motifs
-seurat_object <- find_motifs(
-    seurat_object,
+grn_object <- find_motifs(
+    grn_object,
     pfm = motifs,
     genome = BSgenome.Hsapiens.UCSC.hg38
 )
 
 # Infer gene regulatory network
-seurat_object <- infer_grn(seurat_object)
+grn_object <- infer_grn(grn_object)
 
 # Print inferred coefficients
-coef(seurat_object)
+coef(grn_object)
 
 # Find gene and regulatory modules 
-test_srt <- find_modules(test_srt)
+test_srt <- find_modules(grn_object)
 
 # Print modules
 NetworkModules(test_srt)