public override ChromCorrelationData CorrelateData(Run run, IqResult iqResult, int startScan, int stopScan)
{
var correlationData = new ChromCorrelationData();
var o16MzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[0].XValue;
var o18SingleLabelMzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[2].XValue;
var o18DoubleLabelMzValue = iqResult.Target.TheorIsotopicProfile.Peaklist[4].XValue;
var o16ChromXyData = GetBaseChromXYData(run, startScan, stopScan, o16MzValue);
var o18SingleLabelChromXyData = GetBaseChromXYData(run, startScan, stopScan, o18SingleLabelMzValue);
var o18DoubleLabelChromXyData = GetBaseChromXYData(run, startScan, stopScan, o18DoubleLabelMzValue);
double slope, intercept, rsquaredVal;
GetElutionCorrelationData(o16ChromXyData, o18SingleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
GetElutionCorrelationData(o16ChromXyData, o18DoubleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
GetElutionCorrelationData(o18SingleLabelChromXyData, o18DoubleLabelChromXyData, out slope, out intercept, out rsquaredVal);
correlationData.AddCorrelationData(slope, intercept, rsquaredVal);
return(correlationData);
}
public IqResult(IqTarget target)
{
_labelFreeResultExporter = new IqLabelFreeResultExporter();
_childResults = new List <IqResult>();
Target = target;
IqResultDetail = new IqResultDetail();
CorrelationData = new ChromCorrelationData();
FitScore = 1;
InterferenceScore = 1;
IsExported = true;
}
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);
}
private void UpdateIsoIntensitiesUsingChromCorrData(ChromCorrelationData chromCorrelationData, IsotopicProfile iso)
{
var totalChromCorrDataItems = chromCorrelationData.CorrelationDataItems.Count;
double heightMaxPeak = iso.getMostIntensePeak().Height;
for (var i = 0; i < iso.Peaklist.Count; i++)
{
if (i < totalChromCorrDataItems)
{
var correctedRelIntensity = chromCorrelationData.CorrelationDataItems[i].CorrelationSlope;
if (correctedRelIntensity.HasValue)
{
iso.Peaklist[i].Height = (float)(heightMaxPeak * correctedRelIntensity);
}
}
}
}
/// <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);
}
private IsotopicProfile GetIsoDataPassingChromCorrelation(ChromCorrelationData chromCorrelationData, IsotopicProfile iso)
{
var returnedIso = iso.CloneIsotopicProfile();
returnedIso.Peaklist.Clear();
for (var i = 0; i < iso.Peaklist.Count; i++)
{
if (i < chromCorrelationData.CorrelationDataItems.Count)
{
if (chromCorrelationData.CorrelationDataItems[i].CorrelationRSquaredVal > MinimumRSquaredValForQuant)
{
returnedIso.Peaklist.Add(iso.Peaklist[i]);
}
else
{
break;
}
}
}
return(returnedIso);
}
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);
}
/// <summary>
/// Performs charge correlation on all peaks within a sequence level target
/// </summary>
/// <param name="targetList"></param>
/// <param name="run"></param>
/// <param name="correlationThreshold"></param>
/// <param name="peaksToCorrelate"></param>
/// <returns></returns>
public ChargeCorrelationData CorrelateData(List <ChromPeakIqTarget> targetList, Run run, double correlationThreshold = 0.8, int peaksToCorrelate = 3)
{
var correlationList = new List <ChargeCorrelationItem>();
var availableTargets = new List <ChromPeakIqTarget>(targetList);
//Sorts target list by fit score
//Lowest to Highest
var sortedTargetList = targetList.OrderBy(n => n.GetResult().FitScore);
foreach (var referenceTarget in sortedTargetList)
{
//Checks to see if reference peak is in availableTargets list
if (!availableTargets.Contains(referenceTarget))
{
continue;
}
//New ChargeCorrelationItem for the reference peak
var referenceCorrelationData = new ChargeCorrelationItem(referenceTarget);
//Gets the ChromPeaks base width in scans for correlation
int startScan, stopScan;
GetBaseScanRange(referenceTarget.ChromPeak, out startScan, out stopScan);
//Generates an array of XICs for the reference peak
var referenceMZList = DeconTools.Backend.Utilities.IsotopicProfileUtilities.GetTopNMZValues(referenceTarget.TheorIsotopicProfile.Peaklist, peaksToCorrelate);
var referenceXIC = GetCorrelationXICs(peaksToCorrelate, referenceMZList, run, startScan, stopScan);
//Iterates through the rest of the available targets
foreach (var correlatingTarget in targetList)
{
//Checks if target is available
if (!availableTargets.Contains(correlatingTarget))
{
continue;
}
//Checks if the peak to be correlated has an XValue that falls within the base peak range of the reference peak
if (correlatingTarget.ChromPeak.XValue > startScan && correlatingTarget.ChromPeak.XValue < stopScan)
{
//Generates an XIC array for the peak being correlated.
var correlationMZList =
DeconTools.Backend.Utilities.IsotopicProfileUtilities.GetTopNMZValues(
correlatingTarget.TheorIsotopicProfile.Peaklist, peaksToCorrelate);
var correlationXIC = GetCorrelationXICs(peaksToCorrelate, correlationMZList, run, startScan, stopScan);
//Generates new correlation data item for current correlation
var correlationData = new ChromCorrelationData();
for (var i = 0; i < peaksToCorrelate; i++)
{
//Checks if either of the XICs are null
if (referenceXIC[i] != null && correlationXIC[i] != null)
{
double slope, intercept, rsquaredval;
GetElutionCorrelationData(referenceXIC[i],
FillInAnyMissingValuesInChromatogram(referenceXIC[i].Xvalues, correlationXIC[i]), out slope,
out intercept, out rsquaredval);
correlationData.AddCorrelationData(slope, intercept, rsquaredval);
}
else
{
//A placeholder to show that the data was poor
correlationData.AddCorrelationData(-9999, -9999, 0);
}
}
//Checks if the overall correlation median is higher than the correlation threshold
if (correlationData.RSquaredValsMedian >= correlationThreshold)
{
referenceCorrelationData.PeakCorrelationData.Add(correlatingTarget, correlationData);
//Removes correlating target from the availableTargets list because it was successfully correlated.
availableTargets.Remove(correlatingTarget);
}
}
}
//Removes reference target from availableTargets list
availableTargets.Remove(referenceTarget);
correlationList.Add(referenceCorrelationData);
}
var chargeCorrelationData = new ChargeCorrelationData();
chargeCorrelationData.CorrelationData = correlationList;
return(chargeCorrelationData);
}