From be31f654a57b22a0c1463e3032bf9c9b28785d26 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Thu, 23 Apr 2026 23:42:56 -0400
Subject: [PATCH] make run order determine levels of run

---
 R/MSstatsConvert_core_functions.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/MSstatsConvert_core_functions.R b/R/MSstatsConvert_core_functions.R
index c5e98c77..3d9ee7dc 100644
--- a/R/MSstatsConvert_core_functions.R
+++ b/R/MSstatsConvert_core_functions.R
@@ -571,7 +571,10 @@ MSstatsAnomalyScores = function(input, quality_metrics, temporal_direction,
     
     subset_cols = subset_cols[subset_cols %in% names(input)]
     input = input[, ..subset_cols]
-    
+
+    ordered_runs = .standardizeColnames(run_order$Run[order(run_order$Order)])
+    input$Run = factor(input$Run, levels = ordered_runs)
+
     return(input)
 
 }