private IList <DataRowDetails> SumMs1Transitions(IList <DataRowDetails> dataRows)
{
var dataRowsByReplicateIndexAndTransitionGroup =
dataRows.ToLookup(row =>
new Tuple <int, IdentityPath>(row.ReplicateIndex,
row.IdentityPath.GetPathTo((int)SrmDocument.Level.TransitionGroups)));
var newDataRows = new List <DataRowDetails>();
foreach (var grouping in dataRowsByReplicateIndexAndTransitionGroup)
{
DataRowDetails ms1DataRow = null;
var transitionGroup = (TransitionGroupDocNode)SrmDocument.FindNode(grouping.Key.Item2);
foreach (var dataRow in grouping)
{
var transition = (TransitionDocNode)transitionGroup.FindNode(dataRow.IdentityPath.Child);
if (transition.IsMs1)
{
if (ms1DataRow == null)
{
ms1DataRow = new DataRowDetails()
{
IdentityPath = grouping.Key.Item2,
BioReplicate = dataRow.BioReplicate,
Control = dataRow.Control,
ReplicateIndex = dataRow.ReplicateIndex
};
}
ms1DataRow.Intensity += dataRow.Intensity;
ms1DataRow.Denominator += dataRow.Denominator;
}
else
{
newDataRows.Add(dataRow);
}
}
if (ms1DataRow != null)
{
newDataRows.Add(ms1DataRow);
}
}
return(newDataRows);
}
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);
}
}
}
}