public SipperQuantifier()
{
ChromToleranceInPPM = 25;
NumPointsInSmoother = 7;
MinimumRelativeIntensityForChromCorr = 0.0001;
_chromatogramCorrelatorTask = new ChromatogramCorrelator(NumPointsInSmoother, MinimumRelativeIntensityForChromCorr,
(int)ChromToleranceInPPM);
_labelingDistributionCalculator = new LabelingDistributionCalculator();
_partialLabelingQuantifier = new PartialLabelingQuantifier("C", 12, 13)
{
MaxLabelAmount = 15,
StepAmountForIterator = 0.25,
NumLeftZeroPads = 1,
NumRightZeroPads = 1,
IsTheoreticalTrimmedDownToObserved = true
};
IsChromatogramCorrelationPerformed = true;
MaximumFitScoreForFurtherProcessing = 0.50;
MinimumRatioAreaForFurtherProcessing = 5;
MinimumRSquaredValForQuant = 0.75;
ChromatogramRSquaredVals = new List <double>();
RatioVals = new XYData();
FitScoreData = new Dictionary <decimal, double>();
}
public SipperQuantifierOld()
{
IsChromatogramCorrelationPerformed = true;
MaximumFitScoreForFurtherProcessing = 0.50;
MinimumRatioAreaForFurtherProcessing = 5;
MinimumRSquaredValForQuant = 0.75;
MinimumRelativeIntensityForChromCorr = 0.0001;
ChromToleranceInPPM = 25;
const int numPointsInSmoother = 5;
_chromatogramCorrelatorTask = new ChromatogramCorrelator(numPointsInSmoother, MinimumRelativeIntensityForChromCorr, (int)ChromToleranceInPPM);
ChromatogramRSquaredVals = new List <double>();
RatioLogVals = new XYData();
RatioVals = new XYData();
_labelingDistributionCalculator = new LabelingDistributionCalculator();
_partialLabelingQuantifier = new PartialLabelingQuantifier("C", 12, 13);
_partialLabelingQuantifier.MaxLabelAmount = 15;
_partialLabelingQuantifier.StepAmountForIterator = 0.25;
}
public void CalculateLabelingDistributionTest2()
{
//mass_tag_id monoisotopic_mass NET obs mod_count mod_description pmt peptide peptideex
//355176429 1538.8166126 0.42422 1 0 2.00000 LFLASACLYGAALAGV R.LFLASACLYGAALAGV.C
//------------------------load theor data ------------------------------------
var peptideUtils = new PeptideUtils();
var peptide = new PeptideTarget();
peptide.Code = "LFLASACLYGAALAGV";
peptide.EmpiricalFormula = new PeptideUtils().GetEmpiricalFormulaForPeptideSequence(peptide.Code);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
theorFeatureGenerator.GenerateTheorFeature(peptide);
var theorProfile = peptide.IsotopicProfile;
var theorIntensities = theorProfile.Peaklist.Select(p => (double)p.Height).ToList();
Console.WriteLine("Total carbons = " + peptideUtils.GetNumAtomsForElement("C", peptide.EmpiricalFormula));
var obsIntensities = new List <double>(new[]
{
1, 0.8335001, 0.4029815, 0.1846439, 0.1116047, 0.09458135, 0.07157851, 0.04972008,
0.03036686, 0.01545749, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
var relexCorrectedIntensities = new List <double>(new[]
{
1, 0.84416, 0.4174013, 0.1843375, 0.1073706, 0.09557419, 0.07190877, 0.04823519,
0.02991197, 0.01456759, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
/*
*
* Data for observed profile:
* LCMSFeature 8517 from Yellow_C13_070_23Mar10_Griffin_10-01-28
* *
* peak mz relIntens width sn
* 0 770.418569278349 1 0.008119391 285.256
* 1 770.919748892834 0.8335001 0.008161238 884.9909
* 2 771.421020812818 0.4029815 0.008248929 566.6187
* 3 771.922575912402 0.1846439 0.008058954 703.6938
* 4 772.424544684666 0.1116047 0.007997629 358.0133
* 5 772.926348484216 0.09458135 0.008128829 677.3434
* 6 773.428080290323 0.07157851 0.008151106 100
* 7 773.929769365137 0.04972008 0.008104968 100
* 8 774.431542463583 0.03036686 0.007982519 100
* 9 774.933237566856 0.01545749 0.008024476 100
* 10 775.434950373045 0.008299164 0.008166174 740.9502
* 11 775.936532837365 0.004003931 0.007899459 100
* 12 776.438361528879 0.001711554 0.00877683 44.79652
* 13 776.940072709136 0.0007663054 0.007601836 17.12788
* 14 777.441663634739 0.0004845143 0.007320933 100
*
*/
var labelDistCalc = new LabelingDistributionCalculator();
double[] solvedXVals;
double[] solvedYvals;
var d = 0.1;
labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
var xydata = new XYData();
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("threshold= " + d);
xydata.Display();
labelDistCalc.CalculateLabelingDistribution(theorIntensities, relexCorrectedIntensities, d, d, out solvedXVals, out solvedYvals);
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("Relex-corrected isotopic profile= " + d);
xydata.Display();
double fractionUnlabelled, fractionLabelled, averageLabelsIncorporated;
labelDistCalc.OutputLabelingInfo(solvedYvals.ToList(), out fractionUnlabelled, out fractionLabelled,
out averageLabelsIncorporated);
Console.WriteLine();
Console.WriteLine("fractionUnlabelled= " + fractionUnlabelled);
Console.WriteLine("fractionLabelled= " + fractionLabelled);
Console.WriteLine("averageAmountLabelIncorp= " + averageLabelsIncorporated);
//for (double d = 0; d < 2.1; d+=0.1)
//{
// labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
// XYData xydata = new XYData();
// xydata.Xvalues = solvedXVals;
// xydata.Yvalues = solvedYvals;
// Console.WriteLine();
// Console.WriteLine("threshold= " + d);
// xydata.Display();
//}
}
public void CalculateLabelingDistributionTest1()
{
// LabelDistribution calculation is based on John Chik's work
// He provided a standard set of data here: http://people.ucalgary.ca/~dschriem/CalcDeut/CalcDeut/
// We will use his test values and pass it through our implementation
/*
*#<<<Isotope Calculation Result >>>
#Formula: ISO:|VDWCPTGF| H2O + (H)1
#Resolution: 10000 resolving power
#Threshold (%): 1.0000
#Isotope List - 5 Mass(es)
#
#Isotope Mass Relative Intensity
# 924.39202 100.0000
# 925.39495 53.0190
# 926.39553 20.6161
# 927.39655 5.9286
# 928.39781 1.3694
*/
//observed: (from J. Chik's data) 118.8932 73.8074 34.413 14.4563 6.3169
/*
* Output Data from 'CalcDeut' testing from Dave Schriemer's data (see link above)
* File: MS924.3_Z1_10.0-10.2_A344-351_dist.xml
*
* <DeutDist startdeut='-0.0' chisq='5.80293903626e-05' content_type='numlist' distsum='1.00331024913' entries='5'>
* 0.832945525577
* 0.0747772118716
* 0.0305125766799
* 0.0704222225599
* -0.00534728755986
* </DeutDist>
*
*
*/
var theorIntensities = new List <double>(new[] { 1, 0.530190, 0.206161, 0.059286, 0.013694 });
var obsIntensities = new List <double>(new[] { 118.8932, 73.8074, 34.413, 14.4563, 6.3169 });
var labelDistCalc = new LabelingDistributionCalculator();
double[] solvedXVals;
double[] solvedYvals;
var intensityThreshold = 0.01;
labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, intensityThreshold, intensityThreshold, out solvedXVals, out solvedYvals,
truncateTheorBasedOnRelIntensity: false,
truncateObservedBasedOnRelIntensity: false,
leftPadding: 0,
rightPadding: 2,
numPeaksForAbsoluteTheorList: 3,
numPeaksForAbsoluteObsList: 5);
Assert.AreEqual(0.8329455, Math.Round(solvedYvals[0]), 7);
Assert.AreEqual(0.0747772, Math.Round(solvedYvals[1]), 7);
Assert.AreEqual(0.0305126, Math.Round(solvedYvals[2]), 7);
Assert.AreEqual(0.0704222, Math.Round(solvedYvals[3]), 7);
Assert.AreEqual(-0.0053473, Math.Round(solvedYvals[4]), 7);
var xydata = new XYData();
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
xydata.Display();
double fractionUnlabelled, fractionLabelled, averageLabelsIncorporated;
labelDistCalc.OutputLabelingInfo(solvedYvals.ToList(), out fractionUnlabelled, out fractionLabelled,
out averageLabelsIncorporated);
Console.WriteLine();
Console.WriteLine("fractionUnlabelled= " + fractionUnlabelled);
Console.WriteLine("fractionLabelled= " + fractionLabelled);
Console.WriteLine("averageAmountLabelIncorp= " + averageLabelsIncorporated);
}
