private void GetChromatogramCorrelationData(SipperLcmsTargetedResult result)
{
_chromScanWindowWidth = result.ChromPeakSelected.Width * 2;
var startScan = result.ScanSet.PrimaryScanNumber - (int)Math.Round(_chromScanWindowWidth / 2, 0);
var stopScan = result.ScanSet.PrimaryScanNumber + (int)Math.Round(_chromScanWindowWidth / 2, 0);
result.ChromCorrelationData = _chromatogramCorrelatorTask.CorrelatePeaksWithinIsotopicProfile(result.Run,
NormalizedIso,
startScan,
stopScan);
ChromatogramRSquaredVals.AddRange(
result.ChromCorrelationData.CorrelationDataItems.Select(p => p.CorrelationRSquaredVal.GetValueOrDefault(-1)).
ToList());
//trim off zeros
for (var i = ChromatogramRSquaredVals.Count - 1; i >= 0; i--)
{
if (ChromatogramRSquaredVals[i] <= 0)
{
ChromatogramRSquaredVals.RemoveAt(i);
}
else
{
break;
}
}
result.ChromCorrelationMin = ChromatogramRSquaredVals.Min();
if (ChromatogramRSquaredVals.Count > 1)
{
//get the best rsquared value other than the base peak's rsquared value (which is always 1)
result.ChromCorrelationMax =
(from n in ChromatogramRSquaredVals orderby n descending select n).ToList().ElementAt(1);
result.ChromCorrelationMedian = MathUtils.GetMedian(ChromatogramRSquaredVals);
result.ChromCorrelationAverage = ChromatogramRSquaredVals.Average();
if (ChromatogramRSquaredVals.Count > 2)
{
result.ChromCorrelationStdev = MathUtils.GetStDev(ChromatogramRSquaredVals);
}
else
{
result.ChromCorrelationStdev = -1;
}
}
else
{
result.ChromCorrelationMax = 1;
}
}
private void GetLinearRegressionData(SipperLcmsTargetedResult result, List <double> xvals, List <double> yvals)
{
var logRatioXVals = new List <double>();
var logRatioYVals = new List <double>();
var foundYvalAboveZero = false;
for (var i = 0; i < xvals.Count; i++)
{
if (yvals[i] > 0)
{
foundYvalAboveZero = true;
logRatioXVals.Add(xvals[i]);
logRatioYVals.Add(Math.Log(yvals[i]));
}
else
{
//if we have already found a yval above 0, and then we found one below 0, this
//indicates a problem which we will penalize.
//if (foundYvalAboveZero)
//{
// logRatioXVals.Add(xvals[i]);
// logRatioYVals.Add(0);
//}
}
}
double slope = -9999;
double intercept = -9999;
double rsquaredVal = -1;
RatioLogVals.Xvalues = logRatioXVals.ToArray();
RatioLogVals.Yvalues = logRatioYVals.ToArray();
if (logRatioYVals.Count > 2)
{
try
{
MathUtils.GetLinearRegression(RatioLogVals.Xvalues, RatioLogVals.Yvalues, out slope, out intercept,
out rsquaredVal);
}
catch (Exception)
{
Console.WriteLine(result.Target.ID + "; Error getting linear regression in Sipper quantifier");
}
}
else
{
rsquaredVal = 0;
}
}
public TargetedResultBase CreateMassTagResult(TargetBase massTag)
{
TargetedResultBase result;
switch (ResultType)
{
case Globals.ResultType.BASIC_TARGETED_RESULT:
result = new MassTagResult(massTag);
break;
case Globals.ResultType.N14N15_TARGETED_RESULT:
result = new N14N15_TResult(massTag);
break;
case Globals.ResultType.O16O18_TARGETED_RESULT:
result = new O16O18TargetedResultObject(massTag);
break;
case Globals.ResultType.SIPPER_TARGETED_RESULT:
result = new SipperLcmsTargetedResult(massTag);
break;
case Globals.ResultType.TOPDOWN_TARGETED_RESULT:
result = new TopDownTargetedResult(massTag);
break;
case Globals.ResultType.DEUTERATED_TARGETED_RESULT:
result = new DeuteratedTargetedResultObject(massTag);
break;
default:
result = new MassTagResult(massTag);
break;
}
this.MassTagResultList.Add(massTag, result);
result.MSFeatureID = MSFeatureCounter;
result.Score = 1;
result.Run = this.Run;
this.MSFeatureCounter++;
return(result);
}
private static void addAdditionalInfo(TargetedResultDTO tr, SipperLcmsTargetedResult result)
{
var r = (SipperLcmsFeatureTargetedResultDTO)tr;
r.MatchedMassTagID = ((LcmsFeatureTarget)result.Target).FeatureToMassTagID;
r.AreaUnderDifferenceCurve = result.AreaUnderDifferenceCurve;
r.AreaUnderRatioCurve = result.AreaUnderRatioCurve;
r.AreaUnderRatioCurveRevised = result.AreaUnderRatioCurveRevised;
r.ChromCorrelationMin = result.ChromCorrelationMin;
r.ChromCorrelationMax = result.ChromCorrelationMax;
r.ChromCorrelationAverage = result.ChromCorrelationAverage;
r.ChromCorrelationMedian = result.ChromCorrelationMedian;
r.ChromCorrelationStdev = result.ChromCorrelationStdev;
r.NumCarbonsLabelled = result.NumCarbonsLabelled;
r.PercentPeptideLabelled = result.PercentPeptideLabelled;
r.PercentCarbonsLabelled = result.PercentCarbonsLabelled;
r.NumHighQualityProfilePeaks = result.NumHighQualityProfilePeaks;
r.LabelDistributionVals = result.LabelDistributionVals == null ? null : result.LabelDistributionVals.ToArray();
r.FitScoreLabeledProfile = result.FitScoreLabeledProfile;
r.ContiguousnessScore = result.ContiguousnessScore;
r.RSquaredValForRatioCurve = result.RSquaredValForRatioCurve;
}
private void OutputMassSpectrum(string outputFolder, XYData massSpectrumXYData, TargetBase target, SipperLcmsTargetedResult sipperLcmsTargetedResult)
{
var msGraphGenerator = new MSGraphControl();
msGraphGenerator.SymbolType = SymbolType.None;
if (massSpectrumXYData == null)
{
massSpectrumXYData = new XYData();
massSpectrumXYData.Xvalues = new double[] { 0, 1, 2, 3, 4, 5 };
massSpectrumXYData.Yvalues = new double[] { 0, 1, 2, 3, 4, 5 };
}
msGraphGenerator.GenerateGraph(massSpectrumXYData.Xvalues, massSpectrumXYData.Yvalues, target.MZ - 2,
target.MZ + 6);
var annotation = "fractionC13= " + sipperLcmsTargetedResult.PercentCarbonsLabelled.ToString("0.000") + "\n" +
"populationFraction= " + sipperLcmsTargetedResult.PercentPeptideLabelled.ToString("0.000");
msGraphGenerator.AddAnnotationRelativeAxis(annotation, 0.45, 0.05);
var outputFilename = Path.Combine(outputFolder, target.ID + "_MS.png");
msGraphGenerator.SaveGraph(outputFilename);
}
private void GetChromatogramCorrelationData(SipperLcmsTargetedResult result)
{
//NOTE: this is a very important step. If too wide, correlation data will be poor
//and may lead to overly strict treatment of the data
_chromScanWindowWidth = result.ChromPeakSelected.Width / 2.35 * 4;
//TODO: change this!
//_chromScanWindowWidth = 19;
var startScan = result.ScanSet.PrimaryScanNumber - (int)Math.Round(_chromScanWindowWidth / 2, 0);
var stopScan = result.ScanSet.PrimaryScanNumber + (int)Math.Round(_chromScanWindowWidth / 2, 0);
result.ChromCorrelationData = _chromatogramCorrelatorTask.CorrelatePeaksWithinIsotopicProfile(result.Run, NormalizedIso, startScan, stopScan);
if (result.ChromCorrelationData.CorrelationDataItems.Count > 0)
{
ChromatogramRSquaredVals.AddRange(result.ChromCorrelationData.CorrelationDataItems.Select(p => p.CorrelationRSquaredVal.GetValueOrDefault(-1)).ToList());
}
//GORD: remove this console code later
//Console.WriteLine();
//Console.WriteLine(result.Target.ID);
//foreach (var item in result.ChromCorrelationData.CorrelationDataItems)
//{
// Console.WriteLine(item.CorrelationRSquaredVal);
//}
//trim off zeros
for (var i = ChromatogramRSquaredVals.Count - 1; i >= 1; i--)
{
if (ChromatogramRSquaredVals[i] <= 0)
{
ChromatogramRSquaredVals.RemoveAt(i);
}
else
{
break;
}
}
if (ChromatogramRSquaredVals.Count > 1)
{
result.ChromCorrelationMin = ChromatogramRSquaredVals.Min();
//get the best rsquared value other than the base peak's rsquared value (which is always 1)
result.ChromCorrelationMax =
(from n in ChromatogramRSquaredVals orderby n descending select n).ToList().ElementAt(1);
result.ChromCorrelationMedian = MathUtils.GetMedian(ChromatogramRSquaredVals);
result.ChromCorrelationAverage = ChromatogramRSquaredVals.Average();
if (ChromatogramRSquaredVals.Count > 2)
{
result.ChromCorrelationStdev = MathUtils.GetStDev(ChromatogramRSquaredVals);
}
else
{
result.ChromCorrelationStdev = -1;
}
}
else
{
result.ChromCorrelationMin = -1;
result.ChromCorrelationMax = -1;
}
}
