From 6678c781639cec23323dc636c176815ca0f024a0 Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 25 Jul 2025 10:02:15 -0400
Subject: [PATCH] adjust error handling for zero edges and handling of issue
 column

---
 R/utils_getSubnetworkFromIndra.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index 34c4fbb..207b150 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -116,7 +116,9 @@
         }
         input <- input[!is.na(input$log2FC) & abs(input$log2FC) > logfc_cutoff, ]
     }
-    input <- input[is.na(input$issue), ]
+    if ("issue" %in% colnames(input)) {
+        input <- input[is.na(input$issue), ]
+    }
     
     # Combine filtered data with exempt proteins and remove duplicates
     if (!is.null(exempt_proteins) && nrow(exempt_proteins) > 0) {
@@ -295,7 +297,7 @@
         edges <- edges[which(abs(edges$correlation) >= correlation_cutoff), ]
     }
     if (nrow(edges) == 0) {
-        warning("No edges remain after applying filters. Consider relaxing filters")
+        stop("No edges remain after applying filters. Consider relaxing filters")
     }
     return(edges)
 }