public PeptideQuantifier(PeptideGroupDocNode peptideGroup, PeptideDocNode peptideDocNode,
QuantificationSettings quantificationSettings)
{
PeptideGroupDocNode = peptideGroup;
PeptideDocNode = peptideDocNode;
QuantificationSettings = quantificationSettings;
}
private SrmDocument ChangeQuantificationSettings(SrmDocument srmDocument, QuantificationSettings quantificationSettings)
{
return(srmDocument.ChangeSettings(
srmDocument.Settings.ChangePeptideSettings(
srmDocument.Settings.PeptideSettings.ChangeAbsoluteQuantification(
quantificationSettings))));
}
public PeptideQuantifier(Func <NormalizationData> getNormalizationDataFunc, PeptideGroupDocNode peptideGroup, PeptideDocNode peptideDocNode,
QuantificationSettings quantificationSettings)
{
PeptideGroupDocNode = peptideGroup;
PeptideDocNode = peptideDocNode;
QuantificationSettings = quantificationSettings;
_getNormalizationDataFunc = getNormalizationDataFunc;
}
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);
}
}
}
}
