public void CalculateSpeciesAbundanceByLinearRegression()
{
var mergedPeaks = MergeEnvelopes();
int maxLength = Math.Min(PeptideProfile.Count + 4, mergedPeaks.Count);
double[][] a = GetProfileMatrix(maxLength);
double[] x;
this.SpeciesAbundance = CalculateSpeciesAbundance(maxLength, a, mergedPeaks, out x);
double[] theoreticalIntensities = GetTheoreticalIntensities(maxLength, x);
double[] observedIntensities = GetObservedIntensities(maxLength, mergedPeaks);
double corr = StatisticsUtils.PearsonCorrelation(theoreticalIntensities, observedIntensities);
this.SpeciesAbundance.RegressionCorrelation = corr;
this.SpeciesAbundance.RegressionItems.Clear();
int pepCharge = GetCharge();
var gap = (Atom.O18.MonoMass - Atom.O.MonoMass) / pepCharge;
var gapC = (Atom.C13.MonoMass - Atom.C.MonoMass) / pepCharge;
double mzO16 = TheoreticalO16Mz;
double mzO181 = TheoreticalO16Mz + gap;
double mzO182 = mzO181 + gap;
double[] mzs = { mzO16, mzO16 + gapC, mzO181, mzO181 + gapC, mzO182, mzO182 + gapC };
for (int i = 0; i < maxLength && i < mzs.Length; i++)
{
var ri = new SpeciesRegressionItem();
ri.Mz = mzs[i];
ri.ObservedIntensity = observedIntensities[i];
ri.RegressionIntensity = theoreticalIntensities[i];
this.SpeciesAbundance.RegressionItems.Add(ri);
}
var calc = this.GetCalculator();
this.SampleAbundance = calc.Calculate(this.SpeciesAbundance);
}
public O18QuantificationSummaryItem ReadFromFile(string filename)
{
var result = new O18QuantificationSummaryItem();
var root = XElement.Load(filename);
result.RawFilename = root.Element("RawFilename").Value;
var ele = root.Element("SoftwareVersion");
if (ele != null)
{
result.SoftwareVersion = ele.Value;
}
result.PeptideSequence = root.Element("PeptideSequence").Value;
result.AdditionalFormula = root.Element("AdditionalFormula").Value;
result.PeptideAtomComposition = root.Element("PeptideAtomComposition").Value;
result.PurityOfO18Water = MyConvert.ToDouble(root.Element("PurityOfO18Water").Value);
result.IsPostDigestionLabelling = bool.Parse(root.Element("IsPostDigestionLabelling").Value);
if (root.Element("TheoreticalO16Mz") != null)
{
result.TheoreticalO16Mz = MyConvert.ToDouble(root.Element("TheoreticalO16Mz").Value);
result.Charge = Convert.ToInt32(root.Element("Charge").Value);
}
result.PeptideProfile = (from x in root.Element("PeptideProfile").Elements()
let mzEle = x.Attribute("Mz")
let mz = mzEle == null ? 0.0 : MyConvert.ToDouble(mzEle.Value)
let intensity = MyConvert.ToDouble(x.Value)
select new Peak(mz, intensity)).ToList();
if (result.PeptideProfile[0].Mz == 0.0)
{
var pkls = IsotopicBuilderFactory.GetBuilder().GetProfile(new AtomComposition(result.PeptideAtomComposition), result.Charge, 10);
for (int i = 0; i < Math.Min(result.PeptideProfile.Count, pkls.Count); i++)
{
result.PeptideProfile[i].Mz = pkls[i].Mz;
result.PeptideProfile[i].Intensity = pkls[i].Intensity;
}
}
var observed = root.Element("ObservedEnvelopes");
result.ObservedEnvelopes = new List <O18QuanEnvelope>();
foreach (var pkl in observed.Elements())
{
var peakList = new O18QuanEnvelope();
int scan = int.Parse(pkl.Attribute("Scan").Value);
double retentiontime = MyConvert.ToDouble(pkl.Attribute("Retentiontime").Value);
peakList.Enabled = bool.Parse(pkl.Attribute("Enabled").Value);
peakList.IsIdentified = bool.Parse(pkl.Attribute("Identified").Value);
peakList.ScanTimes.Add(new ScanTime(scan, retentiontime));
foreach (var peak in pkl.Elements())
{
double mz = MyConvert.ToDouble(peak.Attribute("Mz").Value);
double intensity = MyConvert.ToDouble(peak.Attribute("Intensity").Value);
var p = new Peak(mz, intensity);
peakList.Add(p);
}
result.ObservedEnvelopes.Add(peakList);
}
var species = root.Element("SpeciesAbundance");
result.SpeciesAbundance.O16 = MyConvert.ToDouble(species.Element("O16").Value);
result.SpeciesAbundance.O181 = MyConvert.ToDouble(species.Element("O181").Value);
result.SpeciesAbundance.O182 = MyConvert.ToDouble(species.Element("O182").Value);
var regression = species.Element("Regression");
result.SpeciesAbundance.RegressionCorrelation = MyConvert.ToDouble(regression.Attribute("Correlation").Value);
result.SpeciesAbundance.RegressionItems.Clear();
foreach (var item in regression.Elements())
{
var ritem = new SpeciesRegressionItem();
ritem.Mz = MyConvert.ToDouble(item.Attribute("Mz").Value);
ritem.ObservedIntensity = MyConvert.ToDouble(item.Attribute("Observed").Value);
ritem.RegressionIntensity = MyConvert.ToDouble(item.Attribute("Regression").Value);
result.SpeciesAbundance.RegressionItems.Add(ritem);
}
var samples = root.Element("SampleAbundance");
result.SampleAbundance.LabellingEfficiency = MyConvert.ToDouble(samples.Attribute("LabellingEfficiency").Value);
result.SampleAbundance.Ratio = MyConvert.ToDouble(samples.Attribute("Ratio").Value);
result.SampleAbundance.O16 = MyConvert.ToDouble(samples.Element("O16").Value);
result.SampleAbundance.O18 = MyConvert.ToDouble(samples.Element("O18").Value);
return(result);
}
