/// <summary> /// Finds the XIC based on the m/z and scan parameters. /// </summary> /// <param name="mz"></param> /// <param name="scan"></param> /// <returns></returns> public List <XYData> FindXic(double mz, int scan, bool shouldSmooth) { LcmsFeatureTarget target = new LcmsFeatureTarget(); target.ID = 0; target.MZ = mz; target.ScanLCTarget = scan; target.ElutionTimeUnit = Globals.ElutionTimeUnit.ScanNum; m_run.CurrentMassTag = target; var result = m_run.ResultCollection.GetTargetedResult(m_run.CurrentMassTag); double chromPeakGeneratorTolInPPM = MzPpmWindow; Globals.ChromatogramGeneratorMode chromGeneratorMode = Globals.ChromatogramGeneratorMode.MZ_BASED; var chromGen = new PeakChromatogramGenerator(chromPeakGeneratorTolInPPM, chromGeneratorMode); chromGen.NETWindowWidthForNonAlignedData = Convert.ToSingle(NetWindow); int pointsToSmooth = 5; var chromSmoother = new SavitzkyGolaySmoother(pointsToSmooth, 2); double chromPeakDetectorPeakBR = 1; double chromPeakDetectorSigNoise = 1; var chromPeakDetector = new ChromPeakDetector(chromPeakDetectorPeakBR, chromPeakDetectorSigNoise); ChromPeakSelectorParameters chromPeakSelectorParameters = new ChromPeakSelectorParameters(); var chromPeakSelector = new BasicChromPeakSelector(chromPeakSelectorParameters); //this generates an extracted ion chromatogram // Since we are not using the built in generator, chromGen.Execute(m_run.ResultCollection); //this smooths the data - very important step! if (shouldSmooth) { chromSmoother.Execute(m_run.ResultCollection); } //this detects peaks within an extracted ion chromatogram chromPeakDetector.Execute(m_run.ResultCollection); //this selects the peak chromPeakSelector.Parameters.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget; chromPeakSelector.Execute(m_run.ResultCollection); //Here's the chromatogram data... List <XYData> data = new List <XYData>(); for (int i = 0; i < m_run.XYData.Xvalues.Length; i++) { XYData datum = new XYData(m_run.XYData.Xvalues[i], m_run.XYData.Yvalues[i]); data.Add(datum); } return(data); }
public PeakChromatogramGenerator(double tolerance, Globals.ChromatogramGeneratorMode chromMode, Globals.IsotopicProfileType isotopicProfileTarget, Globals.ToleranceUnit toleranceUnit = Globals.ToleranceUnit.PPM) { Tolerance = tolerance; ChromatogramGeneratorMode = chromMode; IsotopicProfileTarget = isotopicProfileTarget; TopNPeaksLowerCutOff = 0.3; ChromWindowWidthForNonAlignedData = 0.4f; ChromWindowWidthForAlignedData = 0.1f; ToleranceUnit = toleranceUnit; _chromGen = new ChromatogramGenerator(); }
public PeakChromatogramGenerator(double tolerance, Globals.ChromatogramGeneratorMode chromMode) : this(tolerance, chromMode, Globals.IsotopicProfileType.UNLABELED) { }