Added additional outputs to PEP engine (#2424)

Co-authored-by: Nic Bollis <[email protected]>

MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs

@@ -161,7 +161,10 @@ public string ComputePEPValuesForAllPSMs()
  sumOfAllAmbiguousPeptidesResolved += ambiguousPeptidesResolved;
  }
 
- return AggregateMetricsForOutput(allMetrics, sumOfAllAmbiguousPeptidesResolved);
+ int positiveTrainingCount = PSMDataGroups.SelectMany(p => p).Count(p => p.Label);
+ int negativeTrainingcount = PSMDataGroups.SelectMany(p => p).Count(p => !p.Label);
+
+ return AggregateMetricsForOutput(allMetrics, sumOfAllAmbiguousPeptidesResolved, positiveTrainingCount, negativeTrainingcount, QValueCutoff);
  }
 
  /// <summary>
@@ -331,7 +334,8 @@ public IEnumerable<PsmData> CreatePsmData(string searchType,
  return pda.AsEnumerable();
  }
 
- public static string AggregateMetricsForOutput(List<CalibratedBinaryClassificationMetrics> allMetrics, int sumOfAllAmbiguousPeptidesResolved)
+ public static string AggregateMetricsForOutput(List<CalibratedBinaryClassificationMetrics> allMetrics, int sumOfAllAmbiguousPeptidesResolved,
+ int positiveTrainingCount, int negativeTrainingCount, double qValueCutoff)
  {
  List<double> accuracy = allMetrics.Select(m => m.Accuracy).ToList();
  List<double> areaUnderRocCurve = allMetrics.Select(m => m.AreaUnderRocCurve).ToList();
@@ -381,6 +385,9 @@ public static string AggregateMetricsForOutput(List<CalibratedBinaryClassificati
  s.AppendLine("* NegativePrecision: " + negativePrecision.Average().ToString());
  s.AppendLine("* NegativeRecall: " + negativeRecall.Average().ToString());
  s.AppendLine("* Count of Ambiguous Peptides Removed: " + sumOfAllAmbiguousPeptidesResolved.ToString());
+ s.AppendLine("* Q-Value Cutoff for Training Targets: " + qValueCutoff);
+ s.AppendLine("* Targets Used for Training: " + positiveTrainingCount.ToString());
+ s.AppendLine("* Decoys Used for Training: " + negativeTrainingCount.ToString());
  s.AppendLine("************************************************************");
  return s.ToString();
  }