From c07170d6a14010e16d374f041ed7d8c9e3fe4714 Mon Sep 17 00:00:00 2001
From: Yancong Zhang <yancongz@outlook.com>
Date: Fri, 28 Apr 2023 12:34:19 -0400
Subject: [PATCH] Fixed issue for cases where there are no features retained
 after filtering

---
 NEWS         |  3 +++
 R/MTXmodel.R | 25 +++++++++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/NEWS b/NEWS
index 42ae3df..6b4b3ca 100755
--- a/NEWS
+++ b/NEWS
@@ -1,6 +1,9 @@
 
 # MTXmodel History #
 
+## Changes in v1.2.3 (2023-04-28) ##
+* Fixed issue if no features left after filtering
+
 ## Changes in v1.2.2 (2022-11-14) ##
 * Fixed warning on if conditions
 * Fixed issue for sample matching
diff --git a/R/MTXmodel.R b/R/MTXmodel.R
index f3d3584..5b75d08 100755
--- a/R/MTXmodel.R
+++ b/R/MTXmodel.R
@@ -1006,6 +1006,31 @@ MTXmodel <-
             }
         }
         
+		if (ncol(filtered_data_norm) < 1) { 
+            all_outfile <- file.path(output, "all_results.tsv")
+            mycolnames = c( 
+                "feature",
+                "metadata",
+                "value",
+                "coef",
+                "stderr",
+                "N", 
+                "N.not.0",
+                "pval",
+                "qval")
+            write.table(
+                t(mycolnames),
+                file = all_outfile,
+                sep = "\t",
+                quote = FALSE,
+                col.names = FALSE,
+                row.names = FALSE)
+
+            residuals_file = file.path(output, "residuals.rds")
+            file.create(residuals_file)
+            return(NULL)
+        }		
+
         # apply the method to the data with the correction
         logging::loginfo(
             "Running selected analysis method: %s", analysis_method)