public void Calculate(IIdentifiedProteinGroup proteinGroup, Func <IIdentifiedSpectrum, bool> validFunc)
{
List <IIdentifiedSpectrum> spectra = (from s in proteinGroup[0].GetSpectra()
where s.GetRatioEnabled() && validFunc(s)
select s).ToList();
QuantificationItem item;
if (spectra.Count == 1)
{
item = spectra[0].GetQuantificationItem();
}
else if (spectra.Count > 1)
{
var sampleIntensities = new List <double>();
var refIntensities = new List <double>();
spectra.ForEach(m =>
{
sampleIntensities.Add(m.GetQuantificationItem().SampleIntensity);
refIntensities.Add(m.GetQuantificationItem().ReferenceIntensity);
});
var intensities = new double[2][];
intensities[0] = refIntensities.ToArray();
intensities[1] = sampleIntensities.ToArray();
LinearRegressionRatioResult lrrr = LinearRegressionRatioCalculator.CalculateRatio(intensities);
item = new QuantificationItem();
item.Ratio = lrrr.Ratio;
item.Correlation = lrrr.RSquare;
double sampleIntensity, refIntensity;
if (lrrr.Ratio > 1)
{
sampleIntensity = sampleIntensities.Max();
refIntensity = sampleIntensity / lrrr.Ratio;
}
else
{
refIntensity = refIntensities.Max();
sampleIntensity = refIntensity * lrrr.Ratio;
}
item.SampleIntensity = sampleIntensity;
item.ReferenceIntensity = refIntensity;
item.Enabled = true;
}
else
{
item = new QuantificationItem();
item.Enabled = false;
}
foreach (IIdentifiedProtein protein in proteinGroup)
{
protein.SetQuantificationItem(item);
}
}
public static LinearRegressionRatioResult GetRegression(this PointPairList pplTotal)
{
double[][] intensities = new double[2][];
intensities[0] = (from ppl in pplTotal
select ppl.X).ToArray();
intensities[1] = (from ppl in pplTotal
select ppl.Y).ToArray();
return(LinearRegressionRatioCalculator.CalculateRatio(intensities));
}
private void CalculateRatio()
{
double[][] intensities = GetIntensityArray();
if (intensities[0].Length <= 1)
{
Ratio = 1;
Distance = 0;
RegressionCorrelation = 0;
return;
}
if (intensities[0].Distinct().Count() == 1 || intensities[1].Distinct().Count() == 1)
{
var avea = intensities[0].Average();
var aveb = intensities[1].Average();
if (avea == 0.0 || aveb == 0.0)
{
Ratio = 1;
Distance = 0;
RegressionCorrelation = 0;
return;
}
Ratio = aveb / avea;
Distance = 0;
RegressionCorrelation = 0;
return;
}
LinearRegressionRatioResult lrrr;
if (_deductBaseLine)
{
lrrr = LinearRegressionRatioCalculator.CalculateRatio(intensities);
}
else
{
lrrr = LinearRegressionRatioCalculator.CalculateRatioDistance(intensities);
}
Ratio = lrrr.Ratio;
Distance = lrrr.Distance;
RegressionCorrelation = lrrr.RSquare;
}
public void CalculateRatio()
{
double[][] intensities = GetIntensityArray();
if (intensities[0].Length > 0)
{
LinearRegressionRatioResult lrrr = LinearRegressionRatioCalculator.CalculateRatio(intensities);
Ratio = lrrr.Ratio;
RegressionCorrelation = lrrr.RSquare;
}
else
{
Ratio = 1.0;
RegressionCorrelation = 0.0;
}
InitAbundanceFromEnvelopes();
}
public QuantificationItem Calculate(IIdentifiedProteinGroup proteinGroup, Func <IIdentifiedSpectrum, bool> validFunc)
{
List <IIdentifiedSpectrum> spectra = (from s in proteinGroup[0].GetSpectra()
where s.IsEnabled(true) && validFunc(s)
select s).ToList();
if (spectra.Count == 1)
{
var item = spectra[0].GetQuantificationItem();
return(new QuantificationItem()
{
Enabled = true,
Ratio = item.Ratio,
Correlation = item.Correlation,
SampleIntensity = item.SampleIntensity,
ReferenceIntensity = item.ReferenceIntensity
});
}
if (spectra.Count > 1)
{
var sampleIntensities = new List <double>();
var refIntensities = new List <double>();
spectra.ForEach(m =>
{
sampleIntensities.Add(m.GetQuantificationItem().SampleIntensity);
refIntensities.Add(m.GetQuantificationItem().ReferenceIntensity);
});
var intensities = new double[2][];
intensities[0] = refIntensities.ToArray();
intensities[1] = sampleIntensities.ToArray();
LinearRegressionRatioResult lrrr = LinearRegressionRatioCalculator.CalculateRatio(intensities);
double sampleIntensity, refIntensity;
if (lrrr.Ratio > 1)
{
sampleIntensities.Sort();
sampleIntensity = sampleIntensities[sampleIntensities.Count - 1];
refIntensity = sampleIntensity / lrrr.Ratio;
}
else
{
refIntensities.Sort();
refIntensity = refIntensities[refIntensities.Count - 1];
sampleIntensity = refIntensity * lrrr.Ratio;
}
return(new QuantificationItem()
{
Enabled = true,
Ratio = lrrr.Ratio,
Correlation = lrrr.RSquare,
SampleIntensity = sampleIntensity,
ReferenceIntensity = refIntensity
});
}
return(new QuantificationItem()
{
Enabled = false
});
}
public void Calculate(IIdentifiedProteinGroup proteinGroup, Func <IIdentifiedSpectrum, bool> validFunc)
{
List <IIdentifiedSpectrum> spectra = (from s in proteinGroup[0].GetSpectra()
where validFunc(s) && s.IsEnabled(true) && HasPeptideRatio(s)
select s).ToList();
if (spectra.Count == 1)
{
var r = CalculatePeptideRatio(spectra[0]);
foreach (var protein in proteinGroup)
{
protein.SetEnabled(true);
protein.Annotations[O18QuantificationConstants.O18_RATIO] = new LinearRegressionRatioResult(r, 0.0)
{
PointCount = 1, TValue = 0, PValue = 1
};
protein.Annotations[this.intensityFunc.ReferenceKey] = spectra[0].Annotations[this.intensityFunc.ReferenceKey];
protein.Annotations[this.intensityFunc.SampleKey] = spectra[0].Annotations[this.intensityFunc.SampleKey];
}
}
else if (spectra.Count > 1)
{
var intensities = this.intensityFunc.ConvertToArray(spectra);
double maxA = intensities[0].Max();
double maxB = intensities[1].Max();
LinearRegressionRatioResult ratioResult;
if (maxA == 0.0)
{
ratioResult = new LinearRegressionRatioResult(20, 0.0)
{
PointCount = intensities.Count(), TValue = 0, PValue = 0
};
maxA = maxB / ratioResult.Ratio;
}
else
{
if (maxB == 0.0)
{
ratioResult = new LinearRegressionRatioResult(0.05, 0.0)
{
PointCount = intensities.Count(), TValue = 0, PValue = 0
};
}
else
{
ratioResult = LinearRegressionRatioCalculator.CalculateRatio(intensities);
}
maxB = maxA * ratioResult.Ratio;
}
foreach (IIdentifiedProtein protein in proteinGroup)
{
protein.SetEnabled(true);
protein.Annotations[O18QuantificationConstants.O18_RATIO] = ratioResult;
protein.Annotations[this.intensityFunc.ReferenceKey] = maxA;
protein.Annotations[this.intensityFunc.SampleKey] = maxB;
}
}
else
{
foreach (IIdentifiedProtein protein in proteinGroup)
{
protein.SetEnabled(false);
protein.Annotations.Remove(O18QuantificationConstants.O18_RATIO);
protein.Annotations.Remove(this.intensityFunc.ReferenceKey);
protein.Annotations.Remove(this.intensityFunc.SampleKey);
}
}
}