public void TestAbundancesEqualizeMedians() { SrmDocument testDocument = OpenTestDocument(); var chromatograms = testDocument.Settings.MeasuredResults.Chromatograms; var expected = ReadDataProcessedRows(new StreamReader(OpenTestFile("BrudererSubsetEqualizeMedians_dataProcessedData.csv"))); NormalizationData normalizationData = NormalizationData.GetNormalizationData(testDocument); var mediansByReplicateFileIndex = chromatograms.ToDictionary(chrom => chrom.MSDataFileInfos.First().FileIndex, chrom => normalizationData.GetMedian(chrom.MSDataFileInfos.First().FileId, IsotopeLabelType.light).Value); double medianMedian = new Statistics(mediansByReplicateFileIndex.Values).Median(); VerifyAbundances(testDocument, expected, transitionChromInfo => { if (transitionChromInfo.IsEmpty || transitionChromInfo.IsTruncated.GetValueOrDefault()) { return(null); } if (transitionChromInfo.Area < 1) { return(0); } else { double abundance = Math.Log(transitionChromInfo.Area, 2.0); abundance -= mediansByReplicateFileIndex[transitionChromInfo.FileIndex]; abundance += medianMedian; return(abundance); } }); }
public NormalizationData GetNormalizationData() { var normalizationData = _normalizationData; if (normalizationData == null) { normalizationData = NormalizationData.GetNormalizationData(Document, false, null); Interlocked.CompareExchange(ref _normalizationData, normalizationData, null); } return(_normalizationData); }
public NormalizedValueCalculator(SrmDocument document) { Document = document; _normalizationData = new Lazy <NormalizationData>(() => NormalizationData.GetNormalizationData(document, false, null)); _fileInfos = new Dictionary <ChromFileInfoId, FileInfo>(new IdentityEqualityComparer <ChromFileInfoId>()); if (document.MeasuredResults != null) { var chromatograms = document.Settings.MeasuredResults.Chromatograms; for (int resultsIndex = 0; resultsIndex < chromatograms.Count; resultsIndex++) { foreach (var chromFileInfo in chromatograms[resultsIndex].MSDataFileInfos) { _fileInfos.Add(chromFileInfo.FileId, new FileInfo(chromFileInfo, resultsIndex, document.Settings)); } } } }
public AreaCVRefinementData(SrmDocument document, AreaCVRefinementSettings settings, CancellationToken token, SrmSettingsChangeMonitor progressMonitor = null) { _settings = settings; if (document == null || !document.Settings.HasResults) { return; } var replicates = document.MeasuredResults.Chromatograms.Count; var areas = new List <AreaInfo>(replicates); var annotations = AnnotationHelper.GetPossibleAnnotations(document, settings.Group).ToArray(); if (!annotations.Any() && settings.Group == null) { annotations = new string[] { null } } ; _internalData = new List <InternalData>(); var hasHeavyMods = document.Settings.PeptideSettings.Modifications.HasHeavyModifications; var hasGlobalStandards = document.Settings.HasGlobalStandardArea; var ms1 = settings.MsLevel == AreaCVMsLevel.precursors; // Avoid using not-MS1 with a document that is only MS1 if (!ms1 && document.MoleculeTransitions.All(t => t.IsMs1)) { ms1 = true; } double?qvalueCutoff = null; if (ShouldUseQValues(document)) { qvalueCutoff = _settings.QValueCutoff; } int?minDetections = null; if (_settings.MinimumDetections != -1) { minDetections = _settings.MinimumDetections; } MedianInfo medianInfo = null; int? ratioIndex = null; if (settings.NormalizeOption.IsRatioToLabel) { var isotopeLabelTypeName = (settings.NormalizeOption.NormalizationMethod as NormalizationMethod.RatioToLabel) ?.IsotopeLabelTypeName; ratioIndex = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes.IndexOf(type => type.Name == isotopeLabelTypeName); } if (_settings.NormalizeOption.Is(NormalizationMethod.EQUALIZE_MEDIANS)) { medianInfo = CalculateMedianAreas(document); } NormalizationData normalizationData = null; foreach (var peptideGroup in document.MoleculeGroups) { foreach (var peptide in peptideGroup.Molecules) { if (progressMonitor != null) { progressMonitor.ProcessMolecule(peptide); } if (_settings.PointsType == PointsTypePeakArea.decoys != peptide.IsDecoy) { continue; } CalibrationCurveFitter calibrationCurveFitter = null; CalibrationCurve calibrationCurve = null; IEnumerable <TransitionGroupDocNode> transitionGroups; if (_settings.NormalizeOption == NormalizeOption.CALIBRATED || _settings.NormalizeOption == NormalizeOption.DEFAULT) { if (!peptide.TransitionGroups.Any()) { continue; } var peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(() => { return(normalizationData = normalizationData ?? NormalizationData.GetNormalizationData(document, false, null)); }, document.Settings, peptideGroup, peptide); calibrationCurveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings); transitionGroups = new[] { peptide.TransitionGroups.First() }; if (_settings.NormalizeOption == NormalizeOption.CALIBRATED) { calibrationCurve = calibrationCurveFitter.GetCalibrationCurve(); if (calibrationCurve == null) { continue; } } } else { transitionGroups = peptide.TransitionGroups; } foreach (var transitionGroupDocNode in transitionGroups) { foreach (var a in annotations) { areas.Clear(); if (!Equals(a, _settings.Annotation) && (_settings.Group == null || _settings.Annotation != null)) { continue; } foreach (var replicateIndex in AnnotationHelper.GetReplicateIndices(document, _settings.Group, a)) { if (progressMonitor != null && progressMonitor.IsCanceled()) { throw new OperationCanceledException(); } token.ThrowIfCancellationRequested(); var groupChromInfo = transitionGroupDocNode.GetSafeChromInfo(replicateIndex) .FirstOrDefault(c => c.OptimizationStep == 0); if (groupChromInfo == null) { continue; } if (qvalueCutoff.HasValue) { if (!(groupChromInfo.QValue.HasValue && groupChromInfo.QValue.Value < qvalueCutoff.Value)) { continue; } } double sumArea, normalizedArea; if (calibrationCurveFitter != null) { double?value; if (calibrationCurve != null) { value = calibrationCurveFitter.GetCalculatedConcentration(calibrationCurve, replicateIndex); } else { value = calibrationCurveFitter.GetNormalizedPeakArea( new CalibrationPoint(replicateIndex, null)); } if (!value.HasValue) { continue; } sumArea = value.Value; normalizedArea = value.Value; } else { if (!groupChromInfo.Area.HasValue) { continue; } var index = replicateIndex; sumArea = transitionGroupDocNode.Transitions.Where(t => { if (ms1 != t.IsMs1 || !t.ExplicitQuantitative) { return(false); } var chromInfo = t.GetSafeChromInfo(index) .FirstOrDefault(c => c.OptimizationStep == 0); if (chromInfo == null) { return(false); } if (_settings.Transitions == AreaCVTransitions.best) { return(chromInfo.RankByLevel == 1); } if (_settings.Transitions == AreaCVTransitions.all) { return(true); } return(chromInfo.RankByLevel <= _settings.CountTransitions); // ReSharper disable once PossibleNullReferenceException }).Sum(t => (double)t.GetSafeChromInfo(index) .FirstOrDefault(c => c.OptimizationStep == 0).Area); normalizedArea = sumArea; if (_settings.NormalizeOption.Is(NormalizationMethod.EQUALIZE_MEDIANS)) { normalizedArea /= medianInfo.Medians[replicateIndex] / medianInfo.MedianMedian; } else if (_settings.NormalizeOption.Is(NormalizationMethod.GLOBAL_STANDARDS) && hasGlobalStandards) { normalizedArea = NormalizeToGlobalStandard(document, transitionGroupDocNode, replicateIndex, sumArea); } else if (_settings.NormalizeOption.Is(NormalizationMethod.TIC)) { var denominator = document.Settings.GetTicNormalizationDenominator( replicateIndex, groupChromInfo.FileId); if (!denominator.HasValue) { continue; } normalizedArea /= denominator.Value; } else if (hasHeavyMods && _settings.NormalizeOption.NormalizationMethod is NormalizationMethod .RatioToLabel) { var ci = transitionGroupDocNode.GetSafeChromInfo(replicateIndex) .FirstOrDefault(c => c.OptimizationStep == 0); RatioValue ratioValue = null; if (ratioIndex.HasValue && ratioIndex.Value >= 0 && ratioIndex.Value < ci.Ratios.Count) { ratioValue = ci.Ratios[ratioIndex.Value]; } if (ratioValue == null) { continue; } normalizedArea = ratioValue.Ratio; } } areas.Add(new AreaInfo(sumArea, normalizedArea)); } if (qvalueCutoff.HasValue && minDetections.HasValue && areas.Count < minDetections.Value) { continue; } _settings.AddToInternalData(_internalData, areas, peptideGroup, peptide, transitionGroupDocNode, a); } } } } Data = ImmutableList <CVData> .ValueOf(_internalData.GroupBy(i => i, (key, grouped) => { var groupedArray = grouped.ToArray(); return(new CVData( groupedArray.Select(idata => new PeptideAnnotationPair(idata.PeptideGroup, idata.Peptide, idata.TransitionGroup, idata.Annotation, idata.CV)), key.CVBucketed, key.Area, groupedArray.Length)); }).OrderBy(d => d.CV)); }