Updated PEP to use set seed (42)

MetaMorpheus/EngineLayer/FdrAnalysis/FdrInfo.cs

@@ -10,5 +10,16 @@ public class FdrInfo
  public double QValueNotch { get; set; }
  public double PEP { get; set; }
  public double PEP_QValue { get; set; }
+
+ /// <summary>
+ /// Creates a new FdrInfo object where Q-Values and PEP_Qvalues are set to 2 by default
+ /// This is done to avoid situations where q-values aren't calcualted for a given peptides, but it is still
+ /// reported in the final results. 
+ /// </summary>
+ public FdrInfo()
+ {
+ QValue = 2;
+ PEP_QValue = 2;
+ }
  }
 }

MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs

@@ -22,6 +22,27 @@ namespace EngineLayer
 {
  public class PepAnalysisEngine
  {
+ private int _randomSeed = 42;
+
+ /// <summary>
+ /// This method contains the hyper-parameters that will be used when training the machine learning model
+ /// </summary>
+ /// <returns> Options object to be passed in to the FastTree constructor </returns>
+ public Microsoft.ML.Trainers.FastTree.FastTreeBinaryTrainer.Options BGDTreeOptions =>
+ new Microsoft.ML.Trainers.FastTree.FastTreeBinaryTrainer.Options
+ {
+ NumberOfThreads = 1,
+ NumberOfTrees = 400,
+ MinimumExampleCountPerLeaf = 10,
+ NumberOfLeaves = 20,
+ LearningRate = 0.2,
+ LabelColumnName = "Label",
+ FeatureColumnName = "Features",
+ Seed = _randomSeed,
+ FeatureSelectionSeed = _randomSeed,
+ RandomStart = false
+ };
+
  private static readonly double AbsoluteProbabilityThatDistinguishesPeptides = 0.05;
 
  //These two dictionaries contain the average and standard deviations of hydrophobicitys measured in 1 minute increments accross each raw
@@ -105,10 +126,10 @@ public string ComputePEPValuesForAllPSMs()
  }
  }
 
- MLContext mlContext = new MLContext();
+ MLContext mlContext = new MLContext(seed: _randomSeed);
  TransformerChain<BinaryPredictionTransformer<Microsoft.ML.Calibrators.CalibratedModelParametersBase<Microsoft.ML.Trainers.FastTree.FastTreeBinaryModelParameters, Microsoft.ML.Calibrators.PlattCalibrator>>>[] trainedModels = new TransformerChain<BinaryPredictionTransformer<Microsoft.ML.Calibrators.CalibratedModelParametersBase<Microsoft.ML.Trainers.FastTree.FastTreeBinaryModelParameters, Microsoft.ML.Calibrators.PlattCalibrator>>>[numGroups];
 
- var trainer = mlContext.BinaryClassification.Trainers.FastTree(labelColumnName: "Label", featureColumnName: "Features", numberOfTrees: 400);
+ var trainer = mlContext.BinaryClassification.Trainers.FastTree(BGDTreeOptions);
  var pipeline = mlContext.Transforms.Concatenate("Features", TrainingVariables)
  .Append(trainer);
 

MetaMorpheus/EngineLayer/PeptideSpectralMatch.cs

@@ -47,6 +47,10 @@ protected PeptideSpectralMatch(SpectralMatch psm, List<(int Notch, IBioPolymerWi
  : base(psm, bestMatchingPeptides)
  {
  }
+
+ public PeptideSpectralMatch(SpectralMatch psm) : base(psm)
+ {
+ }
  #endregion
 
 

MetaMorpheus/EngineLayer/SpectralMatch.cs

@@ -379,6 +379,46 @@ protected SpectralMatch(SpectralMatch psm, List<(int Notch, IBioPolymerWithSetMo
  SpectralAngle = psm.SpectralAngle;
  }
 
+ public SpectralMatch(SpectralMatch psm)
+ {
+ _BestMatchingBioPolymersWithSetMods = psm._BestMatchingBioPolymersWithSetMods;
+ BaseSequence = PsmTsvWriter.Resolve(_BestMatchingBioPolymersWithSetMods.Select(b => b.Pwsm.BaseSequence)).ResolvedValue;
+ FullSequence = PsmTsvWriter.Resolve(_BestMatchingBioPolymersWithSetMods.Select(b => b.Pwsm.FullSequence)).ResolvedValue;
+
+ ModsChemicalFormula = psm.ModsChemicalFormula;
+ Notch = psm.Notch;
+ BioPolymerWithSetModsLength = psm.BioPolymerWithSetModsLength;
+ OneBasedStartResidue = psm.OneBasedStartResidue;
+ OneBasedEndResidue = psm.OneBasedEndResidue;
+ BioPolymerWithSetModsMonoisotopicMass = psm.BioPolymerWithSetModsMonoisotopicMass;
+ ParentLength = psm.ParentLength;
+ Accession = psm.Accession;
+ Organism = psm.Organism;
+ MatchedFragmentIons = psm.MatchedFragmentIons;
+ PsmCount = psm.PsmCount;
+ ModsIdentified = psm.ModsIdentified;
+ LocalizedScores = psm.LocalizedScores;
+ ScanNumber = psm.ScanNumber;
+ PrecursorScanNumber = psm.PrecursorScanNumber;
+ ScanRetentionTime = psm.ScanRetentionTime;
+ ScanExperimentalPeaks = psm.ScanExperimentalPeaks;
+ TotalIonCurrent = psm.TotalIonCurrent;
+ ScanPrecursorCharge = psm.ScanPrecursorCharge;
+ ScanPrecursorMonoisotopicPeakMz = psm.ScanPrecursorMonoisotopicPeakMz;
+ ScanPrecursorMass = psm.ScanPrecursorMass;
+ FullFilePath = psm.FullFilePath;
+ ScanIndex = psm.ScanIndex;
+ FdrInfo = psm.FdrInfo;
+ Score = psm.Score;
+ Xcorr = psm.Xcorr;
+ RunnerUpScore = psm.RunnerUpScore;
+ IsDecoy = psm.IsDecoy;
+ IsContaminant = psm.IsContaminant;
+ DigestionParams = psm.DigestionParams;
+ BioPolymersWithSetModsToMatchingFragments = psm.BioPolymersWithSetModsToMatchingFragments;
+ SpectralAngle = psm.SpectralAngle;
+ }
+
  #endregion
 
  #region FDR

MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs

@@ -137,10 +137,37 @@
  // this could cause weird PSM FDR issues
 
  Status("Estimating PSM FDR...", Parameters.SearchTaskId);
- new FdrAnalysisEngine(psms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters, 
- new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
 
+ List<int> psmsAboveQ = new List<int>();
+ List<int> peptidesAboveQ = new List<int>();
+ List<int> psmsAbovePepQ = new List<int>();
+ List<int> peptidesAbovePepQ = new List<int>();
+
+ for (int i = 0; i < 10; i++)
+ {
+ var tempPsms = psms
+ .Select(p => new PeptideSpectralMatch(p))
+ .Cast<SpectralMatch>()
+ .ToList(); 
+ new FdrAnalysisEngine(tempPsms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters,
+ new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
+ psmsAboveQ.Add(tempPsms.Count(p => p.FdrInfo.QValue <= 0.01));
+ peptidesAboveQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.QValue <= 0.01));
+ psmsAbovePepQ.Add(tempPsms.Count(p => p.FdrInfo.PEP_QValue <= 0.01));
+ peptidesAbovePepQ.Add(tempPsms.Count(p => p.PeptideFdrInfo.PEP_QValue <= 0.01));
+ }
+
+ // write summary text
+ using(StreamWriter writer = new StreamWriter(@"C:\Users\Alex\PEP_NoRandomOrdering.tsv"))
+ {
+ writer.WriteLine("PSMs Q\tPeptides Q\tPSMs PEP-Q\tPeptides PEP-Q");
+ for(int i = 0; i < 10; i++)
+ {
+ writer.WriteLine(String.Join('\t', psmsAboveQ[i], peptidesAboveQ[i], psmsAbovePepQ[i], peptidesAbovePepQ[i]));
+ }
+ }
+ throw new Exception("PEP Seed Results written to file");
  Status("Done estimating PSM FDR!", Parameters.SearchTaskId);
  }
 
  private void ProteinAnalysis()