public void TestRatioToStandard()
{
var doc = LoadTestDocument();
foreach (var peptideGroup in doc.MoleculeGroups)
{
foreach (var peptide in peptideGroup.Peptides)
{
var peptideQuantifier = new PeptideQuantifier(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).Values,
peptideQuantifier.NormalizationMethod).Value;
Assert.AreEqual(expected, actual, .0001, "Error on replicate {0}", replicateIndex);
}
}
}
}
private void GetDataRows(GroupComparisonSelector selector, IList <DataRowDetails> foldChangeDetails)
{
foreach (var replicateEntry in _replicateIndexes)
{
if (!replicateEntry.Value.IsControl &&
!Equals(selector.GroupIdentifier, replicateEntry.Value.GroupIdentifier))
{
continue;
}
foreach (var peptide in selector.ListPeptides())
{
QuantificationSettings quantificationSettings = QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(ComparisonDef.NormalizationMethod)
.ChangeMsLevel(selector.MsLevel);
var peptideQuantifier = new PeptideQuantifier(GetNormalizationData, selector.Protein, peptide,
quantificationSettings)
{
QValueCutoff = ComparisonDef.QValueCutoff
};
if (null != selector.LabelType)
{
peptideQuantifier.MeasuredLabelTypes = ImmutableList.Singleton(selector.LabelType);
}
foreach (var quantityEntry in peptideQuantifier.GetTransitionIntensities(SrmDocument.Settings,
replicateEntry.Key, ComparisonDef.UseZeroForMissingPeaks))
{
var dataRowDetails = new DataRowDetails
{
BioReplicate = replicateEntry.Value.BioReplicate,
Control = replicateEntry.Value.IsControl,
IdentityPath = quantityEntry.Key,
Intensity = Math.Max(1.0, quantityEntry.Value.Intensity),
Denominator = Math.Max(1.0, quantityEntry.Value.Denominator),
ReplicateIndex = replicateEntry.Key,
};
foldChangeDetails.Add(dataRowDetails);
}
}
}
}
