From 2dfc240e26e12c89eef6e2161c7aa4e47e81f693 Mon Sep 17 00:00:00 2001
From: Ryan Corces <ryancorces@gmail.com>
Date: Tue, 10 May 2022 20:50:47 -0700
Subject: [PATCH 1/2] add name to peakSet / PeakMatrix

addressing https://github.com/GreenleafLab/ArchR/discussions/1421 and https://github.com/GreenleafLab/ArchR/issues/308#issuecomment-792338095
---
 R/ProjectMethods.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/ProjectMethods.R b/R/ProjectMethods.R
index 0ac8258c..a64d62f0 100644
--- a/R/ProjectMethods.R
+++ b/R/ProjectMethods.R
@@ -388,6 +388,9 @@ addPeakSet <- function(
       x
     }) %>% Reduce("c", .) %>% sortSeqlevels %>% sort
 
+    #Name each peak
+    peakSet$name <- paste0(seqnames(ps),"_peak",ps$idx)
+    
     #Get NucleoTide Content
     peakSet <- tryCatch({
       .requirePackage("Biostrings",source="bioc")

From 2fc790f800c457ffe78af1772678003aaeb4629d Mon Sep 17 00:00:00 2001
From: Ryan Corces <ryancorces@gmail.com>
Date: Wed, 11 May 2022 11:41:42 -0700
Subject: [PATCH 2/2] dont overwrite peakset name if already exists

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

diff --git a/R/ProjectMethods.R b/R/ProjectMethods.R
index a64d62f0..5e42a5fb 100644
--- a/R/ProjectMethods.R
+++ b/R/ProjectMethods.R
@@ -389,7 +389,9 @@ addPeakSet <- function(
     }) %>% Reduce("c", .) %>% sortSeqlevels %>% sort
 
     #Name each peak
-    peakSet$name <- paste0(seqnames(ps),"_peak",ps$idx)
+    if(is.null(peakSet$name)) {
+      peakSet$name <- paste0(seqnames(ps),"_peak",ps$idx)
+    }
     
     #Get NucleoTide Content
     peakSet <- tryCatch({