add override qValue threshold for unit testing

smith-chem-wisc · Oct 15, 2024 · 5186b82 · 5186b82
1 parent 5231c70
commit 5186b82
Showing 1 changed file with 6 additions and 4 deletions.
diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -14,11 +14,12 @@ public class FdrAnalysisEngine : MetaMorpheusEngine
         private readonly string AnalysisType;
         private readonly string OutputFolder; // used for storing PEP training models  
         private readonly bool DoPEP;
+        private readonly bool QvalueThresholdOverride;
         private readonly int PsmCountThresholdForInvertedQvalue = 1000;
 
         public FdrAnalysisEngine(List<SpectralMatch> psms, int massDiffAcceptorNumNotches, CommonParameters commonParameters,
             List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, List<string> nestedIds, string analysisType = "PSM", 
-            bool doPEP = true, string outputFolder = null) : base(commonParameters, fileSpecificParameters, nestedIds)
+            bool doPEP = true, string outputFolder = null, bool qvalueThresholdOverride = false) : base(commonParameters, fileSpecificParameters, nestedIds)
         {
             AllPsms = psms.OrderByDescending(p => p).ToList();
             MassDiffAcceptorNumNotches = massDiffAcceptorNumNotches;
@@ -28,6 +29,7 @@ public FdrAnalysisEngine(List<SpectralMatch> psms, int massDiffAcceptorNumNotche
             if (AllPsms.Any())
                 AddPsmAndPeptideFdrInfoIfNotPresent();
             if (fileSpecificParameters == null) throw new ArgumentNullException("file specific parameters cannot be null");
+            QvalueThresholdOverride = qvalueThresholdOverride;
         }
 
         private void AddPsmAndPeptideFdrInfoIfNotPresent()
@@ -72,10 +74,10 @@ private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
                         .Select(b => b.FirstOrDefault())
                         .ToList();
 
-                if (psms.Count > PsmCountThresholdForInvertedQvalue & DoPEP)
+                if ((psms.Count > PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride) & DoPEP)
                 {
                     CalculateQValue(psms, peptideLevelCalculation: false, pepCalculation: false);
-                    if (peptides.Count > PsmCountThresholdForInvertedQvalue)
+                    if (peptides.Count > PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride)
                     {
                         CalculateQValue(peptides, peptideLevelCalculation: true, pepCalculation: false);
 
@@ -200,7 +202,7 @@ public void CalculateQValue(List<SpectralMatch> psms, bool peptideLevelCalculati
             }
             else
             {
-                if(psms.Count < PsmCountThresholdForInvertedQvalue)
+                if(psms.Count < PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride)
                 {
 
                    QValueTraditional(psms, peptideLevelAnalysis: peptideLevelCalculation);