From 2cdf42fcd999034810e4f454428e59a0b16b8e52 Mon Sep 17 00:00:00 2001
From: Saori Sakaue <saorisakaue@gmail.com>
Date: Wed, 14 Aug 2024 15:01:31 -0400
Subject: [PATCH] handling no-count-peaks

---
 R/SCENTfunctions.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/SCENTfunctions.R b/R/SCENTfunctions.R
index 1dc102c..0a89055 100644
--- a/R/SCENTfunctions.R
+++ b/R/SCENTfunctions.R
@@ -166,7 +166,9 @@ SCENT_algorithm <- function(object, celltype, ncores, regr = "poisson", bin = TR
 
     #binarize peaks:
     if(bin){
-      atac_target[atac_target$atac>0,]$atac<-1
+      if(nrow(atac_target[atac_target$atac>0,])>0){
+        atac_target[atac_target$atac>0,]$atac<-1
+      }
     }
 
     mrna_target <- object@rna[gene,]