public void TestRatioToStandard()
{
var doc = LoadTestDocument();
foreach (var peptideGroup in doc.MoleculeGroups)
{
foreach (var peptide in peptideGroup.Peptides)
{
var peptideQuantifier = new PeptideQuantifier(null, peptideGroup, peptide,
QuantificationSettings.DEFAULT.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy)));
for (int replicateIndex = 0; replicateIndex < doc.Settings.MeasuredResults.Chromatograms.Count; replicateIndex++)
{
var expected = peptide.Results[replicateIndex].First().LabelRatios.First().Ratio.Ratio;
var actual = PeptideQuantifier.SumQuantities(
peptideQuantifier.GetTransitionIntensities(doc.Settings, replicateIndex, false).Values,
peptideQuantifier.NormalizationMethod).Value;
Assert.AreEqual(expected, actual, .0001, "Error on replicate {0}", replicateIndex);
}
}
}
}
public double?GetNormalizedPeakArea(int replicateIndex)
{
var allTransitionQuantities = GetTransitionQuantities(replicateIndex);
ICollection <PeptideQuantifier.Quantity> quantitiesToSum;
if (!IsAllowMissingTransitions())
{
var completeTransitionSet = GetTransitionsToQuantifyOn();
quantitiesToSum = allTransitionQuantities
.Where(entry => completeTransitionSet.Contains(entry.Key))
.Select(entry => entry.Value)
.ToArray();
if (quantitiesToSum.Count != completeTransitionSet.Count)
{
return(null);
}
}
else
{
quantitiesToSum = allTransitionQuantities.Values;
}
return(PeptideQuantifier.SumQuantities(quantitiesToSum, PeptideQuantifier.NormalizationMethod));
}