From 4f9e99f7f87c7b3fa86b3e8d96b86d95646b3466 Mon Sep 17 00:00:00 2001
From: trishorts <mshort@chem.wisc.edu>
Date: Tue, 15 Oct 2024 15:17:50 -0500
Subject: [PATCH] calculate notch specific inverted qVAlue

---
 .../FdrAnalysis/FdrAnalysisEngine.cs          | 28 +++++++++++++------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
index 576a61bb4..21a1eac5c 100644
--- a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
+++ b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -164,6 +164,7 @@ public void CalculateQValue(List<SpectralMatch> psms, bool peptideLevelCalculati
                 // Stop if canceled
                 if (GlobalVariables.StopLoops) { break; }
 
+                // we have to keep track of q-values separately for each notch
                 int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
                 if (psm.IsDecoy)
                 {
@@ -220,39 +221,50 @@ public void CalculateQValue(List<SpectralMatch> psms, bool peptideLevelCalculati
         private void QValueTraditional(List<SpectralMatch> psms, bool peptideLevelAnalysis)
         {
             double qValue = 0;
-            double qValueNotch = 0;
+            double[] qValueNotch = new double[MassDiffAcceptorNumNotches + 1];
+
             for (int i = 0; i < psms.Count; i++)
             {
                 // Stop if canceled
                 if (GlobalVariables.StopLoops) { break; }
-
+                int notch = psms[i].Notch ?? MassDiffAcceptorNumNotches;
                 qValue = Math.Max(qValue, psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget, 1));
-                qValueNotch = Math.Max(qValueNotch, psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch, 1));
+                qValueNotch[notch] = Math.Max(qValueNotch[notch], psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch, 1));
 
                 psms[i].GetFdrInfo(peptideLevelAnalysis).QValue = Math.Min(qValue, 1);
-                psms[i].GetFdrInfo(peptideLevelAnalysis).QValueNotch = Math.Min(qValueNotch, 1);
+                psms[i].GetFdrInfo(peptideLevelAnalysis).QValueNotch = Math.Min(qValueNotch[notch], 1);
             }
         }
 
-        private static void QValueInverted(List<SpectralMatch> psms, bool peptideLevelAnalysis)
+        private void QValueInverted(List<SpectralMatch> psms, bool peptideLevelAnalysis)
         {
+            double[] qValueNotch = new double[MassDiffAcceptorNumNotches + 1];
+            bool[] qValueNotchCalculated = new bool[MassDiffAcceptorNumNotches + 1];
             psms.Reverse();
             //this calculation is performed from bottom up. So, we begin the loop by computing qValue
             //and qValueNotch for the last/lowest scoring psm in the bunch
             double qValue = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget;
-            double qValueNotch = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch;
+            //double qValueNotch = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch;
 
             //Assign FDR values to PSMs
             for (int i = 0; i < psms.Count; i++)
             {
                 // Stop if canceled
                 if (GlobalVariables.StopLoops) { break; }
+                int notch = psms[i].Notch ?? MassDiffAcceptorNumNotches;
+
+                // populate the highest q-Value for each notch 
+                if (!qValueNotchCalculated[notch])
+                {
+                    qValueNotch[notch] = (psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch + 1) / psms[0].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch;
+                    qValueNotchCalculated[notch] = true;
+                }
 
                 qValue = Math.Min(qValue, (psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoy + 1) / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTarget, 1));
-                qValueNotch = Math.Min(qValueNotch, (psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch + 1) / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch, 1));
+                qValueNotch[notch] = Math.Min(qValueNotch[notch], (psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeDecoyNotch + 1) / Math.Max(psms[i].GetFdrInfo(peptideLevelAnalysis).CumulativeTargetNotch, 1));
 
                 psms[i].GetFdrInfo(peptideLevelAnalysis).QValue = Math.Min(qValue, 1);
-                psms[i].GetFdrInfo(peptideLevelAnalysis).QValueNotch = Math.Min(qValueNotch, 1);
+                psms[i].GetFdrInfo(peptideLevelAnalysis).QValueNotch = Math.Min(qValueNotch[notch], 1);
             }
             psms.Reverse(); //we inverted the psms for this calculation. now we need to put them back into the original order
         }