protected override MetaMorpheusEngineResults RunSpecific()
{
FdrAnalysisResults myAnalysisResults = new FdrAnalysisResults(this, AnalysisType);
Status("Running FDR analysis...");
DoFalseDiscoveryRateAnalysis(myAnalysisResults);
myAnalysisResults.PsmsWithin1PercentFdr = AllPsms.Count(b => b.FdrInfo.QValue <= 0.01 && !b.IsDecoy);
return(myAnalysisResults);
}
protected override MetaMorpheusEngineResults RunSpecific()
{
FdrAnalysisResults myAnalysisResults = new FdrAnalysisResults(this);
Status("Running FDR analysis...");
DoFalseDiscoveryRateAnalysis(newPsms, massDiffAcceptorNumNotches, calculateEValue);
myAnalysisResults.PsmsWithin1PercentFdr = newPsms.Count(b => b.FdrInfo.QValue < 0.01);
return(myAnalysisResults);
}
private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
return;
}
// calculate FDR on a per-protease basis (targets and decoys for a specific protease)
var psmsGroupedByProtease = AllPsms.GroupBy(p => p.DigestionParams.Protease);
foreach (var proteasePsms in psmsGroupedByProtease)
{
var psms = proteasePsms.ToList();
// generate the null distribution for e-value calculations
double globalMeanScore = 0;
int globalMeanCount = 0;
if (CalculateEValue && psms.Any())
{
List <double> combinedScores = new List <double>();
foreach (PeptideSpectralMatch psm in psms)
{
psm.AllScores.Sort();
combinedScores.AddRange(psm.AllScores);
//remove top scoring peptide
if (combinedScores.Any())
{
combinedScores.RemoveAt(combinedScores.Count - 1);
}
}
if (combinedScores.Any())
{
globalMeanScore = combinedScores.Average();
globalMeanCount = (int)((double)combinedScores.Count / psms.Count);
}
else
{
// should be a very rare case... if there are PSMs but each PSM only has one hit
globalMeanScore = 0;
globalMeanCount = 0;
}
}
//Calculate delta scores for the psms (regardless of if we are using them)
foreach (PeptideSpectralMatch psm in psms)
{
if (psm != null)
{
psm.CalculateDeltaScore(ScoreCutoff);
}
}
//determine if Score or DeltaScore performs better
if (UseDeltaScore)
{
const double qValueCutoff = 0.01; //optimize to get the most PSMs at a 1% FDR
List <PeptideSpectralMatch> scoreSorted = psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int ScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
scoreSorted = psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int DeltaScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
//sort by best method
myAnalysisResults.DeltaScoreImprovement = DeltaScorePSMs > ScorePSMs;
psms = myAnalysisResults.DeltaScoreImprovement ?
psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList() :
psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
}
else //sort by score
{
psms = psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
}
double cumulativeTarget = 0;
double cumulativeDecoy = 0;
//set up arrays for local FDRs
double[] cumulativeTargetPerNotch = new double[MassDiffAcceptorNumNotches + 1];
double[] cumulativeDecoyPerNotch = new double[MassDiffAcceptorNumNotches + 1];
//Assign FDR values to PSMs
for (int i = 0; i < psms.Count; i++)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
PeptideSpectralMatch psm = psms[i];
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.IsDecoy)
{
// the PSM can be ambiguous between a target and a decoy sequence
// in that case, count it as the fraction of decoy hits
// e.g. if the PSM matched to 1 target and 2 decoys, it counts as 2/3 decoy
double decoyHits = 0;
double totalHits = 0;
var hits = psm.BestMatchingPeptides.GroupBy(p => p.Peptide.FullSequence);
foreach (var hit in hits)
{
if (hit.First().Peptide.Protein.IsDecoy)
{
decoyHits++;
}
totalHits++;
}
cumulativeDecoy += decoyHits / totalHits;
cumulativeDecoyPerNotch[notch] += decoyHits / totalHits;
}
else
{
cumulativeTarget++;
cumulativeTargetPerNotch[notch]++;
}
double qValue = Math.Min(1, cumulativeDecoy / cumulativeTarget);
double qValueNotch = Math.Min(1, cumulativeDecoyPerNotch[notch] / cumulativeTargetPerNotch[notch]);
double maximumLikelihood = 0;
double eValue = 0;
double eScore = 0;
if (CalculateEValue)
{
eValue = GetEValue(psm, globalMeanCount, globalMeanScore, out maximumLikelihood);
eScore = -Math.Log(eValue, 10);
}
psm.SetFdrValues(cumulativeTarget, cumulativeDecoy, qValue, cumulativeTargetPerNotch[notch], cumulativeDecoyPerNotch[notch], qValueNotch, maximumLikelihood, eValue, eScore, CalculateEValue);
}
// set q-value thresholds such that a lower scoring PSM can't have
// a higher confidence than a higher scoring PSM
//Populate min qValues
double qValueThreshold = 1.0;
double[] qValueNotchThreshold = new double[MassDiffAcceptorNumNotches + 1];
for (int i = 0; i < qValueNotchThreshold.Length; i++)
{
qValueNotchThreshold[i] = 1.0;
}
for (int i = psms.Count - 1; i >= 0; i--)
{
PeptideSpectralMatch psm = psms[i];
// threshold q-values
if (psm.FdrInfo.QValue > qValueThreshold)
{
psm.FdrInfo.QValue = qValueThreshold;
}
else if (psm.FdrInfo.QValue < qValueThreshold)
{
qValueThreshold = psm.FdrInfo.QValue;
}
// threshold notch q-values
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.FdrInfo.QValueNotch > qValueNotchThreshold[notch])
{
psm.FdrInfo.QValueNotch = qValueNotchThreshold[notch];
}
else if (psm.FdrInfo.QValueNotch < qValueNotchThreshold[notch])
{
qValueNotchThreshold[notch] = psm.FdrInfo.QValueNotch;
}
}
}
if (AnalysisType == "PSM")
{
CountPsm();
}
}
private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
return;
}
// generate the null distribution for e-value calculations
double globalMeanScore = 0;
int globalMeanCount = 0;
if (CalculateEValue && Psms.Any())
{
List <double> combinedScores = new List <double>();
foreach (PeptideSpectralMatch psm in Psms)
{
psm.AllScores.Sort();
combinedScores.AddRange(psm.AllScores);
//remove top scoring peptide
if (combinedScores.Any())
{
combinedScores.RemoveAt(combinedScores.Count - 1);
}
}
if (combinedScores.Any())
{
globalMeanScore = combinedScores.Average();
globalMeanCount = (int)((double)combinedScores.Count / Psms.Count);
}
else
{
// should be a very rare case... if there are PSMs but each PSM only has one hit
globalMeanScore = 0;
globalMeanCount = 0;
}
}
int cumulativeTarget = 0;
int cumulativeDecoy = 0;
//Calculate delta scores for the psms (regardless of if we are using them)
foreach (PeptideSpectralMatch psm in Psms)
{
if (psm != null)
{
psm.CalculateDeltaScore(ScoreCutoff);
}
}
//determine if Score or DeltaScore performs better
if (UseDeltaScore)
{
const double qValueCutoff = 0.01; //optimize to get the most PSMs at a 1% FDR
List <PeptideSpectralMatch> scoreSorted = Psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int ScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
scoreSorted = Psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int DeltaScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
//sort by best method BUT DON'T GROUP BECAUSE WE NEED THAT FOR LOCALIZATION
Psms = (DeltaScorePSMs > ScorePSMs) ?
Psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList() :
Psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
myAnalysisResults.DeltaScoreImprovement = DeltaScorePSMs > ScorePSMs;
}
else //sort by score
{
Psms = Psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
}
//set up arrays for local FDRs
int[] cumulativeTargetPerNotch = new int[MassDiffAcceptorNumNotches + 1];
int[] cumulativeDecoyPerNotch = new int[MassDiffAcceptorNumNotches + 1];
//Assign FDR values to PSMs
for (int i = 0; i < Psms.Count; i++)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
var psm = Psms[i];
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.IsDecoy)
{
cumulativeDecoy++;
cumulativeDecoyPerNotch[notch]++;
}
else
{
cumulativeTarget++;
cumulativeTargetPerNotch[notch]++;
}
double qValue = (double)cumulativeDecoy / cumulativeTarget;
double qValueNotch = (double)cumulativeDecoyPerNotch[notch] / cumulativeTargetPerNotch[notch];
double maximumLikelihood = 0;
double eValue = 0;
double eScore = 0;
if (CalculateEValue)
{
eValue = GetEValue(psm, globalMeanCount, globalMeanScore, out maximumLikelihood);
eScore = -Math.Log(eValue, 10);
}
if (qValue > 1)
{
qValue = 1;
}
if (qValueNotch > 1)
{
qValueNotch = 1;
}
psm.SetFdrValues(cumulativeTarget, cumulativeDecoy, qValue, cumulativeTargetPerNotch[notch], cumulativeDecoyPerNotch[notch], qValueNotch, maximumLikelihood, eValue, eScore, CalculateEValue);
}
//Populate min qValues
double min_q_value = double.PositiveInfinity;
double[] min_q_value_notch = new double[MassDiffAcceptorNumNotches + 1];
for (int i = 0; i < MassDiffAcceptorNumNotches + 1; i++)
{
min_q_value_notch[i] = double.PositiveInfinity;
}
//The idea here is to set previous qValues as thresholds,
//such that a lower scoring PSM can't have a higher confidence than a higher scoring PSM
for (int i = Psms.Count - 1; i >= 0; i--)
{
PeptideSpectralMatch psm = Psms[i];
if (psm.FdrInfo.QValue > min_q_value)
{
psm.FdrInfo.QValue = min_q_value;
}
else if (psm.FdrInfo.QValue < min_q_value)
{
min_q_value = psm.FdrInfo.QValue;
}
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.FdrInfo.QValueNotch > min_q_value_notch[notch])
{
psm.FdrInfo.QValueNotch = min_q_value_notch[notch];
}
else if (psm.FdrInfo.QValueNotch < min_q_value_notch[notch])
{
min_q_value_notch[notch] = psm.FdrInfo.QValueNotch;
}
}
}
private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
return;
}
// calculate FDR on a per-protease basis (targets and decoys for a specific protease)
var psmsGroupedByProtease = AllPsms.GroupBy(p => p.DigestionParams.Protease);
foreach (var proteasePsms in psmsGroupedByProtease)
{
var psms = proteasePsms.ToList();
//determine if Score or DeltaScore performs better
if (UseDeltaScore)
{
const double qValueCutoff = 0.01; //optimize to get the most PSMs at a 1% FDR
List <PeptideSpectralMatch> scoreSorted = psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int ScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
scoreSorted = psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => new Tuple <string, int, double?>(b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
int DeltaScorePSMs = GetNumPSMsAtqValueCutoff(scoreSorted, qValueCutoff);
//sort by best method
myAnalysisResults.DeltaScoreImprovement = DeltaScorePSMs > ScorePSMs;
psms = myAnalysisResults.DeltaScoreImprovement ?
psms.OrderByDescending(b => b.DeltaScore).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList() :
psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
}
else //sort by score
{
psms = psms.OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).ToList();
}
double cumulativeTarget = 0;
double cumulativeDecoy = 0;
//set up arrays for local FDRs
double[] cumulativeTargetPerNotch = new double[MassDiffAcceptorNumNotches + 1];
double[] cumulativeDecoyPerNotch = new double[MassDiffAcceptorNumNotches + 1];
//Assign FDR values to PSMs
for (int i = 0; i < psms.Count; i++)
{
// Stop if canceled
if (GlobalVariables.StopLoops)
{
break;
}
PeptideSpectralMatch psm = psms[i];
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.IsDecoy)
{
// the PSM can be ambiguous between a target and a decoy sequence
// in that case, count it as the fraction of decoy hits
// e.g. if the PSM matched to 1 target and 2 decoys, it counts as 2/3 decoy
double decoyHits = 0;
double totalHits = 0;
var hits = psm.BestMatchingPeptides.GroupBy(p => p.Peptide.FullSequence);
foreach (var hit in hits)
{
if (hit.First().Peptide.Protein.IsDecoy)
{
decoyHits++;
}
totalHits++;
}
cumulativeDecoy += decoyHits / totalHits;
cumulativeDecoyPerNotch[notch] += decoyHits / totalHits;
}
else
{
cumulativeTarget++;
cumulativeTargetPerNotch[notch]++;
}
double qValue = Math.Min(1, cumulativeDecoy / cumulativeTarget);
double qValueNotch = Math.Min(1, cumulativeDecoyPerNotch[notch] / cumulativeTargetPerNotch[notch]);
double pep = psm.FdrInfo == null ? double.NaN : psm.FdrInfo.PEP;
double pepQValue = psm.FdrInfo == null ? double.NaN : psm.FdrInfo.PEP_QValue;
psm.SetFdrValues(cumulativeTarget, cumulativeDecoy, qValue, cumulativeTargetPerNotch[notch], cumulativeDecoyPerNotch[notch], qValueNotch, pep, pepQValue);
}
// set q-value thresholds such that a lower scoring PSM can't have
// a higher confidence than a higher scoring PSM
//Populate min qValues
double qValueThreshold = 1.0;
double[] qValueNotchThreshold = new double[MassDiffAcceptorNumNotches + 1];
for (int i = 0; i < qValueNotchThreshold.Length; i++)
{
qValueNotchThreshold[i] = 1.0;
}
for (int i = psms.Count - 1; i >= 0; i--)
{
PeptideSpectralMatch psm = psms[i];
// threshold q-values
if (psm.FdrInfo.QValue > qValueThreshold)
{
psm.FdrInfo.QValue = qValueThreshold;
}
else if (psm.FdrInfo.QValue < qValueThreshold)
{
qValueThreshold = psm.FdrInfo.QValue;
}
// threshold notch q-values
int notch = psm.Notch ?? MassDiffAcceptorNumNotches;
if (psm.FdrInfo.QValueNotch > qValueNotchThreshold[notch])
{
psm.FdrInfo.QValueNotch = qValueNotchThreshold[notch];
}
else if (psm.FdrInfo.QValueNotch < qValueNotchThreshold[notch])
{
qValueNotchThreshold[notch] = psm.FdrInfo.QValueNotch;
}
}
}
if (AnalysisType == "PSM")
{
CountPsm();
if (AllPsms.Count > 0)
{
myAnalysisResults.BinarySearchTreeMetrics = PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(AllPsms);
Compute_PEPValue_Based_QValue(AllPsms);
}
}
if (AnalysisType == "Peptide")
{
Compute_PEPValue_Based_QValue(AllPsms);
}
}
