public double CompareSpectra(MSSpectra spectraX, MSSpectra spectraY)
{
var xIntensities = this.ExpandVector(spectraY.Peaks, spectraX.Peaks).Select(xpeak => xpeak.X).ToArray();
var yIntensities = this.ExpandVector(spectraX.Peaks, spectraY.Peaks).Select(ypeak => ypeak.Y).ToArray();
return(FitScoreCalculator.GetPearsonCorrelation(xIntensities, yIntensities, yIntensities.Length));
}
public double GetRankSumTestPvalue(Ms1Peak[] peaks, int envelopeSize)
{
if (PeakRanking == null)
{
return(1.0d);
}
// calculate ranksum test score
var ranksum = 0;
var nRankSum = 0;
for (var i = 0; i < envelopeSize; i++)
{
if (peaks[i] == null || !peaks[i].Active)
{
continue;
}
var localIndex = peaks[i].IndexInSpectrum - PeakStartIndex;
if (localIndex >= PeakCount || localIndex < 0)
{
continue;
}
ranksum += PeakRanking[localIndex];
nRankSum++;
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(PeakCount, nRankSum, ranksum);
return(pvalue);
}
/// <summary>
/// Get the fit between a theoretical and actual isotopic profile using DeconTools fit score.
/// </summary>
/// <param name="theoretical">The theoretical isotopic profile.</param>
/// <param name="observed">The actual observed isotopic profile.</param>
/// <returns>The DeconTools fit score.</returns>
/// <remarks>0 is the best score, 1 is the worst score.</remarks>
protected override double GetFitScore(double[] theoretical, double[] observed)
{
if (theoretical == null || observed == null || theoretical.Length != observed.Length)
{
return(1.0);
}
return(FitScoreCalculator.GetDeconToolsFit(theoretical, observed));
}
/// <summary>
/// Get the fit between a theoretical and actual isotopic profile using Pearson correlation.
/// </summary>
/// <param name="theoretical">The theoretical isotopic profile.</param>
/// <param name="observed">The actual observed isotopic profile.</param>
/// <returns>The Pearson correlation score.</returns>
/// <remarks>1 is the best score, 0 is the worst score.</remarks>
protected override double GetFitScore(double[] theoretical, double[] observed)
{
if (theoretical == null || observed == null || theoretical.Length != observed.Length)
{
return(0.0);
}
return(FitScoreCalculator.GetPearsonCorrelation(theoretical, observed));
}
public void TestSumIsoProfilesAcrossDifferentCharges()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
if (!File.Exists(TestRawFilePath))
{
Assert.Ignore(@"Skipping test " + methodName + @" since file not found: " + TestRawFilePath);
}
var run = PbfLcMsRun.GetLcMsRun(TestRawFilePath) as PbfLcMsRun;
//var spec = run.GetSpectrum(46452); // 635.37
var spec = run.GetSummedMs1Spectrum(46437, 46466);
var tolerance = new Tolerance(10);
const string protSequence =
"AIPQSVEGQSIPSLAPMLERTTPAVVSVAVSGTHVSKQRVPDVFRYFFGPNAPQEQVQERPFRGLGSGVIIDADKGYIVTNNHVIDGADDIQVGLHDGREVKAKLIGTDSESDIALLQIEAKNLVAIKTSDSDELRVGDFAVAIGNPFGLGQTVTSGIVSALGRSGLGIEMLENFIQTDAAINSGNSGGALVNLKGELIGINTAIVAPNGGNVGIGFAIPANMVKNLIAQIAEHGEVRRGVLGIAGRDLDSQLAQGFGLDTQHGGFVNEVSAGSAAEKAGIKAGDIIVSVDGRAIKSFQELRAKVATMGAGAKVELGLIRDGDKKTVNVTLGEANQTTEKAAGAVHPMLQGASLENASKGVEITDVAQGSPAAMSGLQKGDLIVGINRTAVKDLKSLKELLKDQEGAVALKIVRGKSMLYLVLR";
//const string annotation = "_." + protSequence + "._";
var seqGraph = SequenceGraph.CreateGraph(new AminoAcidSet(), AminoAcid.ProteinNTerm, protSequence, AminoAcid.ProteinCTerm);
if (seqGraph == null)
{
return;
}
seqGraph.SetSink(0);
var neutral = seqGraph.GetSinkSequenceCompositionWithH2O();
var theoProfile = neutral.GetIsotopomerEnvelopeRelativeIntensities();
var expProfile = new double[theoProfile.Length];
for (var charge = 22; charge <= 45; charge++)
{
var ion = new Ion(neutral, charge);
var isotopePeaks = spec.GetAllIsotopePeaks(ion, tolerance, 0.1);
if (isotopePeaks == null)
{
continue;
}
Assert.True(isotopePeaks.Length == theoProfile.Length);
for (var i = 0; i < isotopePeaks.Length; i++)
{
if (isotopePeaks[i] != null)
{
expProfile[i] += isotopePeaks[i].Intensity;
}
}
}
for (var i = 0; i < theoProfile.Length; i++)
{
Console.WriteLine("{0}\t{1}\t{2}", neutral.GetIsotopeMass(i), theoProfile[i], expProfile[i] / expProfile.Max());
}
Console.WriteLine("Corr: " + FitScoreCalculator.GetPearsonCorrelation(theoProfile, expProfile));
}
private double GetHyperGeometricScore()
{
var nPossiblePeaks = Comparer.GetBinNumber(_ms2Spec.Peaks.Last().Mz) - Comparer.GetBinNumber(_ms2Spec.Peaks.First().Mz) + 1;
var nObservedPeaks = _ms2Spec.Peaks.Length;
var pvalue = FitScoreCalculator.GetHyperGeometricPvalue(nPossiblePeaks, nObservedPeaks, _nTheoreticalIonPeaks, _nObservedIonPeaks);
if (pvalue > 0)
{
return(-Math.Log(pvalue, 2));
}
return(50);
}
public void OutputStatistics(ProductSpectrum spectrum, Sequence sequence)
{
var baseIonTypes = spectrum.ActivationMethod != ActivationMethod.ETD ? BaseIonTypesCid : BaseIonTypesEtd;
var cleavages = sequence.GetInternalCleavages().ToArray();
var tolerance = new Tolerance(10);
var maxIntensity = spectrum.Peaks.Max(p => p.Intensity);
foreach (var c in cleavages)
{
foreach (var baseIonType in baseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? c.PrefixComposition + baseIonType.OffsetComposition
: c.SuffixComposition + baseIonType.OffsetComposition;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = spectrum.GetAllIsotopePeaks(ion, tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
continue;
}
var mostAbundantIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
// representative peak intensity
var ionPeakIntensity = observedPeaks[mostAbundantIsotopeIndex].Intensity;
// calc. correlation
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
var corrCoeff = FitScoreCalculator.GetPearsonCorrelation(isotopomerEnvelope, observedIntensities);
// mz error
var mostAbundantIsotopeMz = ion.GetIsotopeMz(mostAbundantIsotopeIndex);
var errorPpm = ((observedPeaks[mostAbundantIsotopeIndex].Mz - mostAbundantIsotopeMz) /
mostAbundantIsotopeMz) * 1e6;
}
}
}
}
/// <summary>
/// Computes the fit score between the ion and corresponding peaks in the spectrum
/// </summary>
/// <param name="ion">ion</param>
/// <param name="tolerance">tolerance</param>
/// <param name="relativeIntensityThreshold">relative intensity threshold of the theoretical isotope profile</param>
/// <returns>fit score</returns>
public double GetFitScore(Ion ion, Tolerance tolerance, double relativeIntensityThreshold = 0.1)
{
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var observedPeaks = GetAllIsotopePeaks(ion, tolerance, relativeIntensityThreshold);
if (observedPeaks == null)
{
return(1);
}
var theoIntensities = new double[observedPeaks.Length];
Array.Copy(isotopomerEnvelope, theoIntensities, theoIntensities.Length);
var maxObservedIntensity = observedPeaks.Select(p => p != null ? p.Intensity : 0).Max();
var normalizedObs = observedPeaks.Select(p => p != null ? p.Intensity / maxObservedIntensity : 0).ToArray();
return(FitScoreCalculator.GetFitOfNormalizedVectors(isotopomerEnvelope, normalizedObs));
}
/// <summary>
/// Get the Bhattacharyya distance and the Pearson correlation for the provided ion and peaks
/// </summary>
/// <param name="ion"></param>
/// <param name="observedPeaks"></param>
/// <returns></returns>
public static Tuple <double, double> GetDistCorr(Ion ion, Peak[] observedPeaks)
{
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var envelope = isotopomerEnvelope;
var observedIntensities = new double[envelope.Length];
for (var i = 0; i < isotopomerEnvelope.Length; i++)
{
if (observedPeaks[i] != null)
{
observedIntensities[i] = observedPeaks[i].Intensity;
}
}
return(FitScoreCalculator.GetDistanceAndCorrelation(envelope, observedIntensities));
//var bcDist = FitScoreCalculator.GetBhattacharyyaDistance(envelope, observedIntensities);
//var corr = FitScoreCalculator.GetPearsonCorrelation(envelope, observedIntensities);
//return new Tuple<double, double>(bcDist, corr);
}
/// <summary>
/// Computes the Pearson correlation between the ion and corresponding peaks in the spectrum
/// </summary>
/// <param name="ion">ion</param>
/// <param name="tolerance">tolerance</param>
/// <param name="relativeIntensityThreshold">relative intensity threshold of the theoretical isotope profile</param>
/// <returns>Pearson correlation</returns>
public double GetCorrScore(Ion ion, Tolerance tolerance, double relativeIntensityThreshold = 0.1)
{
var observedPeaks = GetAllIsotopePeaks(ion, tolerance, relativeIntensityThreshold);
if (observedPeaks == null)
{
return(0);
}
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
return(FitScoreCalculator.GetPearsonCorrelation(isotopomerEnvelope, observedIntensities));
}
/// <summary>
/// Gets the pearson correlation and cosine score of an observed isotopic distribution compared to a theoretical ion.
/// </summary>
/// <param name="ion">Theoretical ion.</param>
/// <param name="observedPeaks">The observed isotopic distribution.</param>
/// <returns>A tuple where the first item is pearson correlation and the second item is cosine.</returns>
private Tuple <double, double> GetCorrCos(Ion ion, Peak[] observedPeaks)
{
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var envelope = isotopomerEnvelope;
var observedIntensities = new double[envelope.Length];
for (var i = 0; i < isotopomerEnvelope.Length; i++)
{
if (observedPeaks[i] != null)
{
observedIntensities[i] = observedPeaks[i].Intensity;
}
}
double pearsonCorrelation = FitScoreCalculator.GetPearsonCorrelation(envelope, observedIntensities);
double cosine = FitScoreCalculator.GetCosine(envelope, observedIntensities);
return(new Tuple <double, double>(pearsonCorrelation, cosine));
}
/// <summary>
/// Get the Pearson correlation of 2 XICs
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
public double GetCorrelation(Xic other)
{
if (Count == 0 || other == null || other.Count == 0)
{
return(0);
}
var count1 = Count;
var count2 = other.Count;
var index1 = 0;
var index2 = 0;
var intList1 = new List <double>();
var intList2 = new List <double>();
while (index1 < count1 && index2 < count2)
{
var comp = this[index1].ScanNum - other[index2].ScanNum;
if (comp < 0)
{
++index1;
}
else if (comp > 0)
{
++index2;
}
else
{
intList1.Add(this[index1].Intensity);
intList2.Add(other[index2].Intensity);
++index1;
++index2;
}
}
var correlation = FitScoreCalculator.GetPearsonCorrelation(intList1.ToArray(), intList2.ToArray());
return(correlation);
}
private double GetRankSumScore()
{
var rankSum = 0d;
var nMatchedIons = _prefixIonPeakIndex.Count + _suffixIonPeakIndex.Count;
var nObservedPeaks = _ms2Spec.Peaks.Length;
foreach (var peakIndex in _prefixIonPeakIndex)
{
rankSum += _peakRanking[peakIndex];
}
foreach (var peakIndex in _suffixIonPeakIndex)
{
rankSum += _peakRanking[peakIndex];
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(nObservedPeaks, nMatchedIons, rankSum);
if (pvalue > 0)
{
return(-Math.Log(pvalue, 2));
}
return(50);
}
/// <summary>
/// Get the Cosine score of 2 XICs
/// </summary>
/// <param name="other"></param>
/// <returns></returns>
public double GetCosine(Xic other)
{
if (Count == 0 || other == null || other.Count == 0)
{
return(0);
}
//var minScanNum = Math.Min(this[0].ScanNum, other[0].ScanNum);
//var maxScanNum = Math.Max(this[Count-1].ScanNum, other[other.Count-1].ScanNum);
var minScanNum = this[0].ScanNum;
var maxScanNum = this[Count - 1].ScanNum;
var intArr1 = new double[maxScanNum - minScanNum + 1];
foreach (var p in this)
{
intArr1[p.ScanNum - minScanNum] = p.Intensity;
}
var intArr2 = new double[maxScanNum - minScanNum + 1];
foreach (var p in other)
{
var index = p.ScanNum - minScanNum;
if (index < 0 || index >= intArr2.Length)
{
continue;
}
intArr2[p.ScanNum - minScanNum] = p.Intensity;
}
var correlation = FitScoreCalculator.GetCosine(intArr1, intArr2);
return(correlation);
}
public void UpdateScore(List <Ms1Spectrum> ms1Spectra, bool pValueCheck = true)
{
var nRows = MaxCharge - MinCharge + 1;
var ms1ScanNumToIndex = _run.GetMs1ScanNumToIndex();
var minCol = ms1ScanNumToIndex[MinScanNum];
var maxCol = ms1ScanNumToIndex[MaxScanNum];
var nCols = maxCol - minCol + 1;
var mostAbuIdx = TheoreticalEnvelope.IndexOrderByRanking[0];
ClearScore();
var bestChargeDist = new double[] { 10.0d, 10.0d };
// sum envelopes at each charge
var summedIntensity = new double[TheoreticalEnvelope.Size];
var xicLen = nCols + 18;
var xicStartIdx = 9;
/*
* if (nCols < 13)
* {
* xicLen = 13;
* xicStartIdx = (int) Math.Floor((xicLen - nCols)*0.5);
* }*/
var xic2 = new double[2][];
xic2[0] = new double[xicLen];
xic2[1] = new double[xicLen];
var chargeXic = new double[nRows][];
var tempBestBcDist = 10.0d;
var repEnvelopeBcDist = 10.0d;
ObservedIsotopeEnvelope repEnvelope = null;
var repEnvelopeBcDist2 = 10.0d;
ObservedIsotopeEnvelope repEnvelope2 = null;
var tempBestDistanceScoreAcrossCharge = new double[2] {
10, 10
};
var tempBestIntensityScoreAcrossCharge = new double[2];
var tempBestCorrelationScoreAcrossCharge = new double[2];
for (var i = 0; i < nRows; i++)
{
var charge = i + MinCharge;
var mostAbuMz = TheoreticalEnvelope.GetIsotopeMz(charge, mostAbuIdx);
Array.Clear(summedIntensity, 0, summedIntensity.Length);
chargeXic[i] = new double[xicLen];
var chargeIdx = (charge % 2 == 0) ? EvenCharge : OddCharge;
var summedMostAbuIsotopeIntensity = 0d;
var summedReferenceIntensity = 0d;
for (var j = 0; j < nCols; j++)
{
var envelope = Envelopes[i][j];
var col = minCol + j;
var localWin = ms1Spectra[col].GetLocalMzWindow(mostAbuMz);
if (envelope == null)
{
continue;
}
envelope.Peaks.SumEnvelopeTo(summedIntensity);
var mostAbuPeak = envelope.Peaks[mostAbuIdx];
if (mostAbuPeak != null && mostAbuPeak.Active)
{
summedMostAbuIsotopeIntensity += mostAbuPeak.Intensity;
summedReferenceIntensity += localWin.HighestIntensity;
}
AbundanceDistributionAcrossCharge[chargeIdx] += envelope.Abundance;
var newBcDist = TheoreticalEnvelope.GetBhattacharyyaDistance(envelope.Peaks);
var newCorr = TheoreticalEnvelope.GetPearsonCorrelation(envelope.Peaks);
var goodEnvelope = (newBcDist <0.07 || newCorr> 0.7);
if (goodEnvelope)
{
xic2[chargeIdx][xicStartIdx + j] += envelope.Abundance;
chargeXic[i][xicStartIdx + j] = envelope.Abundance;
}
var levelOneEnvelope = true;
var levelTwoEnvelope = true;
if (pValueCheck)
{
var poissonPvalue = localWin.GetPoissonTestPvalue(envelope.Peaks, TheoreticalEnvelope.Size);
var rankSumPvalue = localWin.GetRankSumTestPvalue(envelope.Peaks, TheoreticalEnvelope.Size);
levelOneEnvelope = (rankSumPvalue < 0.01 && poissonPvalue < 0.01);
//levelTwoEnvelope = (rankSumPvalue < 0.05 || poissonPvalue < 0.05);
}
if (levelOneEnvelope)
{
if (newBcDist < BestDistanceScoreAcrossCharge[chargeIdx])
{
BestDistanceScoreAcrossCharge[chargeIdx] = newBcDist;
if (localWin.MedianIntensity > 0)
{
BestIntensityScoreAcrossCharge[chargeIdx] = envelope.HighestIntensity / localWin.HighestIntensity;
}
else
{
BestIntensityScoreAcrossCharge[chargeIdx] = 1.0d;
}
}
BestCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(BestCorrelationScoreAcrossCharge[chargeIdx], newCorr);
if (newBcDist < repEnvelopeBcDist)
{
repEnvelopeBcDist = newBcDist;
repEnvelope = envelope;
}
// in the initial scoring, classify major and minor envelopes
if (!_initScore && goodEnvelope)
{
envelope.GoodEnough = true;
}
}
if (levelTwoEnvelope)
{
if (newBcDist < tempBestDistanceScoreAcrossCharge[chargeIdx])
{
tempBestDistanceScoreAcrossCharge[chargeIdx] = newBcDist;
if (localWin.MedianIntensity > 0)
{
tempBestIntensityScoreAcrossCharge[chargeIdx] = envelope.HighestIntensity / localWin.HighestIntensity;
}
else
{
tempBestIntensityScoreAcrossCharge[chargeIdx] = 1.0d;
}
}
tempBestCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(tempBestCorrelationScoreAcrossCharge[chargeIdx], newCorr);
if (newBcDist < repEnvelopeBcDist2)
{
repEnvelopeBcDist2 = newBcDist;
repEnvelope2 = envelope;
}
}
}
var bcDist = TheoreticalEnvelope.GetBhattacharyyaDistance(summedIntensity);
EnvelopeDistanceScoreAcrossCharge[chargeIdx] = Math.Min(bcDist, EnvelopeDistanceScoreAcrossCharge[chargeIdx]);
EnvelopeCorrelationScoreAcrossCharge[chargeIdx] = Math.Max(TheoreticalEnvelope.GetPearsonCorrelation(summedIntensity), EnvelopeCorrelationScoreAcrossCharge[chargeIdx]);
if (BestCharge[chargeIdx] < 1 || bcDist < bestChargeDist[chargeIdx])
{
BestCharge[chargeIdx] = charge;
bestChargeDist[chargeIdx] = bcDist;
if (summedReferenceIntensity > 0)
{
EnvelopeIntensityScoreAcrossCharge[chargeIdx] = summedMostAbuIsotopeIntensity / summedReferenceIntensity;
}
//if (summedMedianIntensity > 0) EnvelopeIntensityScoreAcrossCharge[chargeIdx] = Math.Min(1.0, 0.1*(summedMostAbuIsotopeIntensity / summedMedianIntensity));
}
if (bcDist < tempBestBcDist)
{
tempBestBcDist = bcDist;
Array.Copy(summedIntensity, RepresentativeSummedEnvelop, RepresentativeSummedEnvelop.Length);
}
}
// when good envellope is observed at only either even or odd charge...
if (BestCorrelationScoreAcrossCharge[0] > 0.7 && BestCorrelationScoreAcrossCharge[1] < 0.5)
{
const int i = 1;
BestCorrelationScoreAcrossCharge[i] = tempBestCorrelationScoreAcrossCharge[i];
BestIntensityScoreAcrossCharge[i] = tempBestIntensityScoreAcrossCharge[i];
BestDistanceScoreAcrossCharge[i] = tempBestDistanceScoreAcrossCharge[i];
}
if (BestCorrelationScoreAcrossCharge[1] > 0.7 && BestCorrelationScoreAcrossCharge[0] < 0.5)
{
const int i = 0;
BestCorrelationScoreAcrossCharge[i] = tempBestCorrelationScoreAcrossCharge[i];
BestIntensityScoreAcrossCharge[i] = tempBestIntensityScoreAcrossCharge[i];
BestDistanceScoreAcrossCharge[i] = tempBestDistanceScoreAcrossCharge[i];
}
// normalize abudnace across charges
var s = AbundanceDistributionAcrossCharge[0] + AbundanceDistributionAcrossCharge[1];
if (s > 0)
{
for (var chargeIdx = 0; chargeIdx < 2; chargeIdx++)
{
AbundanceDistributionAcrossCharge[chargeIdx] = AbundanceDistributionAcrossCharge[chargeIdx] / s;
}
}
if (nCols > 1)
{
var evenChargeIdx = BestCharge[EvenCharge] - MinCharge;
var oddChargeIdx = BestCharge[OddCharge] - MinCharge;
XicCorrelationBetweenBestCharges[0] = FitScoreCalculator.GetPearsonCorrelation(Smoother.Smooth(chargeXic[evenChargeIdx]), Smoother.Smooth(chargeXic[oddChargeIdx]));
XicCorrelationBetweenBestCharges[1] = FitScoreCalculator.GetPearsonCorrelation(Smoother.Smooth(xic2[EvenCharge]), Smoother.Smooth(xic2[OddCharge]));
}
if (repEnvelope == null && repEnvelope2 != null)
{
repEnvelope = repEnvelope2;
}
if (repEnvelope != null)
{
// set representative charge, mz and scanNum
RepresentativeCharge = repEnvelope.Charge;
RepresentativeMz = repEnvelope.RepresentativePeak.Mz;
RepresentativeScanNum = repEnvelope.ScanNum;
}
_initScore = true;
}
public void TestFitScoreComputationTime()
{
var methodName = MethodBase.GetCurrentMethod().Name;
Utils.ShowStarting(methodName);
const int numTrials = 1000000;
const int numIsotopes = 20;
var random = new Random();
var theoretical = new double[numTrials][];
var observed = new double[numTrials][];
for (var i = 0; i < numTrials; i++)
{
theoretical[i] = new double[numIsotopes];
observed[i] = new double[numIsotopes];
for (var j = 0; j < numIsotopes; j++)
{
theoretical[i][j] = random.NextDouble();
observed[i][j] = random.NextDouble();
}
}
Console.WriteLine("Calculating fit scores {0} times", numTrials * 2);
var sw = new System.Diagnostics.Stopwatch();
sw.Start();
for (var trial = 0; trial < numTrials; trial++)
{
//FitScoreCalculator.GetDeconToolsFit(theoretical[trial], observed[trial]);
//FitScoreCalculator.GetFitOfNormalizedVectors(theoretical[trial], observed[trial]);
//FitScoreCalculator.GetCosine(theoretical[trial], observed[trial]);
//FitScoreCalculator.GetFitNormalizedByTheoMaxIsotope(theoretical[trial], observed[trial]);
FitScoreCalculator.GetPearsonCorrelation(theoretical[trial], observed[trial]);
}
var series1 = new double[7];
series1[0] = 0.2;
series1[1] = 0.5;
series1[2] = 0.8;
series1[3] = 0.7;
series1[4] = 0.6;
series1[5] = 0.3;
series1[6] = 0.05;
var series2 = new double[series1.Length];
double smallestFit = 1;
var threshold = (int)(1000000 / 10.0);
for (var iteration = 0; iteration < 1000000; iteration++)
{
for (var i = 0; i < series1.Length; i++)
{
series2[i] = series1[i] + random.NextDouble() / 6 - (1 / 12.0);
}
var result = FitScoreCalculator.GetPearsonCorrelation(series1, series2);
if (iteration % threshold == 0)
{
Console.WriteLine(@"Fit=" + result);
}
if (result < smallestFit)
{
smallestFit = result;
}
}
Console.WriteLine(@"SmallestFit=" + smallestFit);
Assert.IsTrue(smallestFit > 0.94);
sw.Stop();
Console.WriteLine(@"Elapsed Time: {0:f4} sec", sw.Elapsed.TotalSeconds);
}
// Select the best peak within +/- filteringWindowSize
public static List <DeconvolutedPeak> GetDeconvolutedPeaks(
Peak[] peaks, int minCharge, int maxCharge,
int isotopeOffsetTolerance, double filteringWindowSize,
Tolerance tolerance, double corrScoreThreshold)
{
var monoIsotopePeakList = new List <DeconvolutedPeak>();
for (var peakIndex = 0; peakIndex < peaks.Length; peakIndex++)
{
var peak = peaks[peakIndex];
// Check whether peak has the maximum intensity within the window
var isBest = true;
var prevIndex = peakIndex - 1;
while (prevIndex >= 0)
{
var prevPeak = peaks[prevIndex];
if ((peak.Mz - prevPeak.Mz) > filteringWindowSize)
{
break;
}
if (prevPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
prevIndex--;
}
if (!isBest)
{
continue;
}
var nextIndex = peakIndex + 1;
while (nextIndex < peaks.Length)
{
var nextPeak = peaks[nextIndex];
if ((nextPeak.Mz - peak.Mz) > filteringWindowSize)
{
break;
}
if (nextPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
nextIndex++;
}
if (!isBest)
{
continue;
}
// peak has the maximum intensity, window = [prevIndex+1,nextIndex-1]
var window = new Peak[nextIndex - prevIndex - 1];
Array.Copy(peaks, prevIndex + 1, window, 0, window.Length);
var windowSpectrum = new Spectrum(window, 1);
var peakMz = peak.Mz;
for (var charge = maxCharge; charge >= minCharge; charge--)
{
var mass = peak.Mz * charge;
var mostAbundantIsotopeIndex = Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex;
for (var isotopeIndex = mostAbundantIsotopeIndex - isotopeOffsetTolerance; isotopeIndex <= mostAbundantIsotopeIndex + isotopeOffsetTolerance; isotopeIndex++)
{
var monoIsotopeMass = Ion.GetMonoIsotopicMass(peakMz, charge, isotopeIndex);
var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(monoIsotopeMass);
var observedPeaks = windowSpectrum.GetAllIsotopePeaks(monoIsotopeMass, charge, isotopomerEnvelope, tolerance, 0.1);
if (observedPeaks == null)
{
continue;
}
var envelop = isotopomerEnvelope.Envolope;
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
var sim = FitScoreCalculator.GetDistanceAndCorrelation(envelop, observedIntensities);
var bcDist = sim.Item1;
var corr = sim.Item2;
if (corr < corrScoreThreshold && bcDist > 0.03)
{
continue;
}
// monoIsotopeMass is valid
var deconvPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
monoIsotopePeakList.Add(deconvPeak);
}
}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
public IsotopeEnvelopeStatisticalInfo PreformStatisticalSignificanceTest(ObservedIsotopeEnvelope envelope)
{
int peakStartIndex;
Tuple <double, double> mzBoundary;
//var refPeak = envelope.Peaks[envelope.RefIsotopeInternalIndex];
var mostAbuMz = 0d;
var mostAbutPeakInternalIndex = envelope.TheoreticalEnvelope.IndexOrderByRanking[0];
if (envelope.Peaks[mostAbutPeakInternalIndex] != null)
{
mostAbuMz = envelope.Peaks[mostAbutPeakInternalIndex].Mz;
}
else
{
mostAbuMz = envelope.TheoreticalEnvelope.GetIsotopeMz(envelope.Charge, mostAbutPeakInternalIndex);
}
var rankings = GetLocalRankings(mostAbuMz, out peakStartIndex, out mzBoundary);
// smallest delta_mz = 0.01 (th) ?
var ret = new IsotopeEnvelopeStatisticalInfo
{
LocalMzStart = mzBoundary.Item1,
LocalMzEnd = mzBoundary.Item2,
NumberOfLocalPeaks = rankings.Length,
NumberOfPossiblePeaks = (int)Math.Ceiling(100 * (mzBoundary.Item2 - mzBoundary.Item1)),
NumberOfIsotopePeaks = envelope.Size,
};
// calculate ranksum test score
var ranksum = 0;
var nRankSum = 0;
for (var i = 0; i < envelope.Size; i++)
{
if (envelope.Peaks[i] == null || !envelope.Peaks[i].Active)
{
continue;
}
ret.NumberOfMatchedIsotopePeaks++;
//if (isotopeList[i].Ratio > RelativeIntesnityThresholdForRankSum)
//{
var localIndex = envelope.Peaks[i].IndexInSpectrum - peakStartIndex;
if (localIndex >= rankings.Length || localIndex < 0)
{
continue;
}
ranksum += rankings[localIndex];
nRankSum++;
//}
}
var pvalue = FitScoreCalculator.GetRankSumPvalue(ret.NumberOfLocalPeaks, nRankSum, ranksum);
ret.RankSumScore = (pvalue > 0) ? -Math.Log(pvalue, 2) : 50;
// calculate poisson test score
var n = ret.NumberOfPossiblePeaks;
var k = ret.NumberOfIsotopePeaks; // # of theretical isotope ions of the mass within the local window
var n1 = ret.NumberOfLocalPeaks; // # of detected ions within the local window
var k1 = ret.NumberOfMatchedIsotopePeaks; // # of matched ions generating isotope envelope profile
var lambda = ((double)n1 / (double)n) * k;
pvalue = 1 - Poisson.CDF(lambda, k1);
ret.PoissonScore = (pvalue > 0) ? -Math.Log(pvalue, 2) : 50;
return(ret);
}
/// <summary>
/// Get the deconvoluted peaks that correspond to the provided peak list
/// </summary>
/// <param name="peaks"></param>
/// <param name="minCharge"></param>
/// <param name="maxCharge"></param>
/// <param name="isotopeOffsetTolerance"></param>
/// <param name="tolerance"></param>
/// <param name="corrScoreThreshold"></param>
/// <returns></returns>
public static List <DeconvolutedPeak> GetDeconvolutedPeaks_new(
Peak[] peaks,
int minCharge,
int maxCharge,
int isotopeOffsetTolerance,
Tolerance tolerance,
double corrScoreThreshold)
{
var spectrum = new Spectrum(peaks, 0);
var monoIsotopePeakList = new List <DeconvolutedPeak>();
var sortedPeaks = peaks.OrderByDescending(peak => peak.Intensity).ToArray();
var peakUsed = new bool[peaks.Length];
foreach (var peak in sortedPeaks)
{
var peakIndex = Array.BinarySearch(peaks, peak);
if (peakUsed[peakIndex])
{
continue;
}
var bestScore = 0.0;
DeconvolutedPeak bestPeak = null;
Tuple <Peak, int>[] bestObservedPeaks = null;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mass = peak.Mz * charge - (charge * Constants.Proton);
if (mass > MaxMass)
{
continue;
}
var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(mass);
var mostAbundantIsotopeIndex = isotopomerEnvelope.MostAbundantIsotopeIndex;
var offsetTolerance = isotopeOffsetTolerance;
if (isotopeOffsetTolerance < 0)
{
offsetTolerance = isotopomerEnvelope.Envelope.Length;
}
for (var isotopeIndex = mostAbundantIsotopeIndex - offsetTolerance;
isotopeIndex <= mostAbundantIsotopeIndex + offsetTolerance;
isotopeIndex++)
{
var monoIsotopeMass = Ion.GetMonoIsotopicMass(peak.Mz, charge, isotopeIndex);
var observedPeaks = GetAllIsotopePeaks(spectrum, monoIsotopeMass, charge, isotopomerEnvelope, tolerance, 0.1);
if (observedPeaks == null)
{
continue;
}
var envelop = isotopomerEnvelope.Envelope;
var observedIntensities = new double[observedPeaks.Length];
var observedPeakCount = 0;
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
if (observedPeak != null && peakUsed[observedPeak.Item2])
{
observedPeak = null;
observedPeaks[i] = null;
}
observedPeakCount += observedPeak != null ? 1 : 0;
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Item1.Intensity : 0.0;
}
var sim = FitScoreCalculator.GetDistanceAndCorrelation(envelop, observedIntensities);
var bcDist = sim.Item1;
var corr = sim.Item2;
var foundPeakRatio = observedPeakCount / ((double)envelop.Length);
var interferenceScore = 10.0;
var filteredObserved = observedPeaks.Where(p => p != null).ToArray();
if (filteredObserved.Length >= 2)
{
var allPeaks =
spectrum.Peaks.Where(p => p.Mz >= filteredObserved[0].Item1.Mz && p.Mz <= filteredObserved[filteredObserved.Length - 1].Item1.Mz).ToArray();
interferenceScore = CalculateInterferenceScore(allPeaks, filteredObserved);
}
bcDist = Math.Max(bcDist, double.Epsilon);
if (corr < corrScoreThreshold && bcDist > 0.1)
{
continue;
}
var score = (foundPeakRatio * corr) / (bcDist * (Math.Abs(mostAbundantIsotopeIndex - isotopeIndex) + 1) * interferenceScore);
//if (corr < corrScoreThreshold) continue;
// monoIsotopeMass is valid
if (score >= bestScore)
{
bestScore = score;
bestPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks.Where(p => p != null).Select(p => p.Item1).ToArray());
bestObservedPeaks = observedPeaks;
}
}
}
if (bestPeak != null)
{
monoIsotopePeakList.Add(bestPeak);
foreach (var p in bestObservedPeaks)
{
if (p != null)
{
bestPeak.ObservedPeakIndices.Add(p.Item2);
peakUsed[p.Item2] = true;
}
}
}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
/// <summary>
/// Get the deconvoluted peaks, selecting the best peak within +/- filteringWindowSize
/// </summary>
/// <param name="scanNum">Scan number (included in any exceptions that are caught)</param>
/// <param name="peaks"></param>
/// <param name="minCharge"></param>
/// <param name="maxCharge"></param>
/// <param name="isotopeOffsetTolerance"></param>
/// <param name="filteringWindowSize"></param>
/// <param name="tolerance"></param>
/// <param name="corrScoreThreshold"></param>
/// <returns></returns>
public static List <DeconvolutedPeak> GetDeconvolutedPeaks(
int scanNum, Peak[] peaks,
int minCharge, int maxCharge,
int isotopeOffsetTolerance, double filteringWindowSize,
Tolerance tolerance, double corrScoreThreshold)
{
try
{
var monoIsotopePeakList = new List <DeconvolutedPeak>();
for (var peakIndex = 0; peakIndex < peaks.Length; peakIndex++)
{
var peak = peaks[peakIndex];
// Check whether peak has the maximum intensity within the window
var isBest = true;
var prevIndex = peakIndex - 1;
while (prevIndex >= 0)
{
var prevPeak = peaks[prevIndex];
if ((peak.Mz - prevPeak.Mz) > filteringWindowSize)
{
break;
}
if (prevPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
prevIndex--;
}
if (!isBest)
{
continue;
}
var nextIndex = peakIndex + 1;
while (nextIndex < peaks.Length)
{
var nextPeak = peaks[nextIndex];
if ((nextPeak.Mz - peak.Mz) > filteringWindowSize)
{
break;
}
if (nextPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
nextIndex++;
}
if (!isBest)
{
continue;
}
// peak has the maximum intensity, window = [prevIndex+1,nextIndex-1]
var window = new Peak[nextIndex - prevIndex - 1];
Array.Copy(peaks, prevIndex + 1, window, 0, window.Length);
var windowSpectrum = new Spectrum(window, 1);
var peakMz = peak.Mz;
//var bestScore = 0.0;
//DeconvolutedPeak bestPeak = null;
for (var charge = maxCharge; charge >= minCharge; charge--)
{
var mass = (peak.Mz * charge) - charge * Constants.Proton;
//var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(mass);
//var mostAbundantIsotopeIndex = isotopomerEnvelope.MostAbundantIsotopeIndex;
var mostAbundantIsotopeIndex = Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex;
for (var isotopeIndex = mostAbundantIsotopeIndex - isotopeOffsetTolerance; isotopeIndex <= mostAbundantIsotopeIndex + isotopeOffsetTolerance; isotopeIndex++)
{
var monoIsotopeMass = Ion.GetMonoIsotopicMass(peakMz, charge, isotopeIndex);
var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(monoIsotopeMass);
var observedPeaks = windowSpectrum.GetAllIsotopePeaks(monoIsotopeMass, charge, isotopomerEnvelope, tolerance, 0.1);
if (observedPeaks == null)
{
continue;
}
var envelop = isotopomerEnvelope.Envelope;
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
var sim = FitScoreCalculator.GetDistanceAndCorrelation(envelop, observedIntensities);
var bcDist = sim.Item1;
var corr = sim.Item2;
//var score = corr / (bcDist * ((double)Math.Abs(isotopeIndex - mostAbundantIsotopeIndex) / envelop.Length));
if (corr < corrScoreThreshold && bcDist > 0.03)
{
continue;
}
// monoIsotopeMass is valid
//if (score >= bestScore)
//{
// bestScore = score;
// bestPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
//}
var deconvPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
monoIsotopePeakList.Add(deconvPeak);
}
}
//if (bestPeak != null)
//{
// monoIsotopePeakList.Add(bestPeak);
//}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
catch (Exception ex)
{
throw new Exception(string.Format("Error getting deconvoluted peaks for scan {0} in GetDeconvolutedPeaks: {1}", scanNum, ex.Message), ex);
}
}