From c5d3223f5c596f531d010f1aa878d53d6a657768 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 2 Mar 2026 15:17:24 +0000
Subject: [PATCH 1/2] Initial plan


From cc2aa3ec44ce04f14a06da8c405703f8d15200ec Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Mon, 2 Mar 2026 15:19:33 +0000
Subject: [PATCH 2/2] Add parameter validation to DIANNtoMSstatsFormat using
 .validateMSstatsConverterParameters

Co-authored-by: devonjkohler <35807256+devonjkohler@users.noreply.github.com>
---
 R/converters_DIANNtoMSstatsFormat.R | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index 82268c8a..55057467 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -79,6 +79,30 @@ DIANNtoMSstatsFormat = function(
     use_log_file = TRUE, append = FALSE, 
     verbose = TRUE, log_file_path = NULL,
     ...) {
+    validation_config = list(
+        input = input,
+        annotation = annotation,
+        qvalue_cutoff = qvalue_cutoff,
+        useUniquePeptide = useUniquePeptide,
+        removeFewMeasurements = removeFewMeasurements,
+        removeProtein_with1Feature = removeProtein_with1Feature,
+        calculateAnomalyScores = calculateAnomalyScores,
+        anomalyModelFeatures = anomalyModelFeatures,
+        anomalyModelFeatureTemporal = anomalyModelFeatureTemporal,
+        removeMissingFeatures = removeMissingFeatures,
+        anomalyModelFeatureCount = anomalyModelFeatureCount,
+        runOrder = runOrder,
+        n_trees = n_trees,
+        max_depth = max_depth,
+        numberOfCores = numberOfCores,
+        use_log_file = use_log_file,
+        append = append,
+        verbose = verbose,
+        log_file_path = log_file_path
+    )
+    
+    .validateMSstatsConverterParameters(validation_config)
+    
     MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, 
                                         log_file_path)