private ChromCorrelationDataItem GetChromCorrDataItem(Run run, int startScan, int stopScan, XYData baseXYData, double correlatedMZValue)
{
bool chromDataIsOK;
var chromPeakXYData = GetCorrelatedChromPeakXYData(run, startScan, stopScan, baseXYData, correlatedMZValue);
chromDataIsOK = chromPeakXYData != null && chromPeakXYData.Xvalues != null &&
chromPeakXYData.Xvalues.Length > 3;
ChromCorrelationDataItem dataItem;
if (chromDataIsOK)
{
double slope;
double intercept;
double rsquaredVal;
chromPeakXYData = FillInAnyMissingValuesInChromatogram(baseXYData, chromPeakXYData);
GetElutionCorrelationData(baseXYData, chromPeakXYData, out slope, out intercept, out rsquaredVal);
dataItem = new ChromCorrelationDataItem(slope, intercept, rsquaredVal);
}
else
{
dataItem = new ChromCorrelationDataItem();
}
return(dataItem);
}
public ChromCorrelationData CorrelateO16O18Profiles(Run run, IsotopicProfile iso, int startScan, int stopScan)
{
var correlationData = new ChromCorrelationData();
var indexO16MonoPeak = 0;
var indexO18SingleLabelPeak = 2;
var indexO18DoubleLabelPeak = 4;
var baseMZValue = iso.Peaklist[indexO16MonoPeak].XValue;
bool baseChromDataIsOK;
var basePeakChromXYData = GetBaseChromXYData(run, startScan, stopScan, baseMZValue);
baseChromDataIsOK = basePeakChromXYData != null && basePeakChromXYData.Xvalues != null &&
basePeakChromXYData.Xvalues.Length > 3;
if (!baseChromDataIsOK)
{
return(new ChromCorrelationData());
}
ChromCorrelationDataItem o18SingleLabelChromCorrDataItem;
if (indexO18SingleLabelPeak >= iso.Peaklist.Count)
{
o18SingleLabelChromCorrDataItem = new ChromCorrelationDataItem();
}
else
{
var correlatedO18SingleLabelMzValue = iso.Peaklist[indexO18SingleLabelPeak].XValue;
o18SingleLabelChromCorrDataItem = GetChromCorrDataItem(run, startScan, stopScan, basePeakChromXYData, correlatedO18SingleLabelMzValue);
}
ChromCorrelationDataItem o18DoubleLabelChromCorrDataItem;
if (indexO18DoubleLabelPeak >= iso.Peaklist.Count)
{
o18DoubleLabelChromCorrDataItem = new ChromCorrelationDataItem();
}
else
{
var correlatedO18DoubleLabelMzValue = iso.Peaklist[indexO18DoubleLabelPeak].XValue;
o18DoubleLabelChromCorrDataItem = GetChromCorrDataItem(run, startScan, stopScan, basePeakChromXYData, correlatedO18DoubleLabelMzValue);
}
correlationData.AddCorrelationData(o18SingleLabelChromCorrDataItem);
correlationData.AddCorrelationData(o18DoubleLabelChromCorrDataItem);
return(correlationData);
}
/// <summary>
/// Selects a peak that correlates with the reference target and returns a bool to continue extending the charge range
/// </summary>
/// <param name="parentTarget"></param>
/// <param name="referenceTarget"></param>
/// <param name="chargeTarget"></param>
/// <param name="correlationCutoff"></param>
/// <param name="fitCutoff"></param>
/// <returns></returns>
private bool ChargeExpansionPeakSelection(TopDownIqTarget parentTarget, ChromPeakIqTarget referenceTarget, IqChargeStateTarget chargeTarget, double correlationCutoff, double fitCutoff)
{
var iqChargeCorrelator = ChromatogramCorrelator as IqChargeCorrelator;
var peakTargets = chargeTarget.ChildTargets();
var sortedPeakTargets = peakTargets.OrderBy(x => x.GetResult().FitScore);
foreach (ChromPeakIqTarget target in sortedPeakTargets)
{
if (referenceTarget.ChromPeak != null)
{
var minScan = referenceTarget.ChromPeak.XValue - (0.5 * referenceTarget.ChromPeak.Width);
var maxScan = referenceTarget.ChromPeak.XValue + (0.5 * +referenceTarget.ChromPeak.Width);
if ((target.ChromPeak.XValue > minScan) && (target.ChromPeak.XValue < maxScan))
{
var correlation = iqChargeCorrelator.PairWiseChargeCorrelation(referenceTarget, target, Run, 3);
if (correlation > correlationCutoff && target.GetResult().FitScore < fitCutoff)
{
UpdateSelection(target);
var parentResult = parentTarget.GetResult() as TopDownIqResult;
foreach (var item in parentResult.ChargeCorrelationData.CorrelationData)
{
if (referenceTarget == item.ReferenceTarget)
{
var corrItem = new ChromCorrelationDataItem(0, 0, correlation);
var corr = new ChromCorrelationData();
corr.AddCorrelationData(corrItem);
item.PeakCorrelationData.Add(target, corr);
}
}
return(true);
}
}
}
}
return(false);
}
public ChromCorrelationData CorrelatePeaksWithinIsotopicProfile(Run run, IsotopicProfile iso, int startScan, int stopScan)
{
var correlationData = new ChromCorrelationData();
var indexMostAbundantPeak = iso.GetIndexOfMostIntensePeak();
var baseMZValue = iso.Peaklist[indexMostAbundantPeak].XValue;
bool baseChromDataIsOK;
var basePeakChromXYData = GetBaseChromXYData(run, startScan, stopScan, baseMZValue);
baseChromDataIsOK = basePeakChromXYData != null && basePeakChromXYData.Xvalues != null;
//&&basePeakChromXYData.Xvalues.Length > 3;
var minIntensity = iso.Peaklist[indexMostAbundantPeak].Height *
MinimumRelativeIntensityForChromCorr;
for (var i = 0; i < iso.Peaklist.Count; i++)
{
if (!baseChromDataIsOK)
{
var defaultChromCorrDataItem = new ChromCorrelationDataItem();
correlationData.AddCorrelationData(defaultChromCorrDataItem);
break;
}
if (i == indexMostAbundantPeak)
{
//peak is being correlated to itself
correlationData.AddCorrelationData(1.0, 0, 1);
}
else if (iso.Peaklist[i].Height >= minIntensity)
{
var correlatedMZValue = iso.Peaklist[i].XValue;
bool chromDataIsOK;
var chromPeakXYData = GetCorrelatedChromPeakXYData(run, startScan, stopScan, basePeakChromXYData, correlatedMZValue);
chromDataIsOK = chromPeakXYData != null && chromPeakXYData.Xvalues != null;
//&&chromPeakXYData.Xvalues.Length > 3;
if (chromDataIsOK)
{
double slope;
double intercept;
double rsquaredVal;
chromPeakXYData = FillInAnyMissingValuesInChromatogram(basePeakChromXYData, chromPeakXYData);
GetElutionCorrelationData(basePeakChromXYData, chromPeakXYData,
out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
}
else
{
var defaultChromCorrDataItem = new ChromCorrelationDataItem();
correlationData.AddCorrelationData(defaultChromCorrDataItem);
}
}
else
{
var defaultChromCorrDataItem = new ChromCorrelationDataItem();
correlationData.AddCorrelationData(defaultChromCorrDataItem);
}
}
return(correlationData);
}
