public ProcessedRowData ComputeAvgTurnover(RawRowData rowData)
{
var result = new ProcessedRowData(rowData)
{
RejectReason = IsAcceptable(rowData),
};
result.InitialPrecursorPool = HalfLifeSettings.InitialPrecursorPool;
if (rowData.MsDataFile.PrecursorPool.HasValue)
{
result.CurrentPrecursorPool = 100 * rowData.MsDataFile.PrecursorPool.Value.DoubleValue;
}
if (!result.CurrentPrecursorPool.HasValue)
{
switch (HalfLifeSettings.PrecursorPoolCalculation)
{
case PrecursorPoolCalculation.Fixed:
result.CurrentPrecursorPool = HalfLifeSettings.CurrentPrecursorPool;
break;
case PrecursorPoolCalculation.MedianPerSample:
double precursorPool;
if (_precursorPools.TryGetValue(rowData.MsDataFile.Id, out precursorPool))
{
result.CurrentPrecursorPool = precursorPool;
}
break;
case PrecursorPoolCalculation.Individual:
result.CurrentPrecursorPool = rowData.IndPrecursorEnrichment * 100;
break;
}
}
switch (HalfLifeSettings.NewlySynthesizedTracerQuantity)
{
case TracerQuantity.LabeledAminoAcid:
result.RawValue = rowData.TracerPercent / 100;
break;
case TracerQuantity.UnlabeledPeptide:
if (rowData.Peaks.Count > 0)
{
result.RawValue = rowData.Peaks[0].Area / rowData.AreaUnderCurve;
}
break;
}
if (!result.CurrentPrecursorPool.HasValue)
{
if (rowData.TracerPercent == result.InitialPrecursorPool)
{
// In an experiment with no labeling, we don't want to reject this item.
// Even if we don't know the CurrentPrecursorPool, we do know that the turnover is 0
result.Turnover = 0;
}
else
{
result.RejectReason = RejectReason.NoPrecursorPool;
return(result);
}
}
else
{
switch (HalfLifeSettings.NewlySynthesizedTracerQuantity)
{
case TracerQuantity.PartialLabelDistribution:
{
var turnoverCalculator = GetTurnoverCalculator(rowData.Peptide.Sequence);
double?turnover;
double?turnoverScore;
turnoverCalculator.ComputeTurnover(result.CurrentPrecursorPool.Value, turnoverCalculator.ToTracerFormulaDict(rowData.PeakAreas), out turnover, out turnoverScore);
result.Turnover = turnover;
result.TurnoverScore = turnoverScore;
}
break;
case TracerQuantity.LabeledAminoAcid:
result.Turnover = (100 * result.RawValue - result.InitialPrecursorPool) /
(result.CurrentPrecursorPool - result.InitialPrecursorPool);
break;
case TracerQuantity.UnlabeledPeptide:
{
var turnoverCalculator = GetTurnoverCalculator(rowData.Peptide.Sequence);
var initialRawValue = turnoverCalculator.ExpectedUnlabeledFraction(result.InitialPrecursorPool);
var finalRawValue = turnoverCalculator.ExpectedUnlabeledFraction(result.CurrentPrecursorPool.Value);
result.Turnover = (result.RawValue - initialRawValue) / (finalRawValue - initialRawValue);
}
break;
}
if (null == result.RejectReason && ValidationStatus.accept != result.RawRowData.ValidationStatus)
{
if (0 < MinTurnoverScore && result.TurnoverScore < MinTurnoverScore)
{
result.RejectReason = RejectReason.LowTurnoverScore;
}
}
}
if (null == result.RejectReason && !result.Turnover.HasValue)
{
result.RejectReason = RejectReason.ValueOutOfRange;
}
return(result);
}
public ProcessedRowData ComputeAvgTurnover(RawRowData rowData)
{
var result = new ProcessedRowData(rowData)
{
RejectReason = IsAcceptable(rowData),
};
result.InitialPrecursorPool = HalfLifeSettings.InitialPrecursorPool;
if (rowData.MsDataFile.PrecursorPool.HasValue)
{
result.CurrentPrecursorPool = 100 * rowData.MsDataFile.PrecursorPool.Value.DoubleValue;
}
if (!result.CurrentPrecursorPool.HasValue)
{
switch (HalfLifeSettings.PrecursorPoolCalculation)
{
case PrecursorPoolCalculation.Fixed:
result.CurrentPrecursorPool = HalfLifeSettings.CurrentPrecursorPool;
break;
case PrecursorPoolCalculation.MedianPerSample:
double precursorPool;
if (_precursorPools.TryGetValue(rowData.MsDataFile.Id, out precursorPool))
{
result.CurrentPrecursorPool = precursorPool;
}
break;
case PrecursorPoolCalculation.Individual:
result.CurrentPrecursorPool = rowData.IndPrecursorEnrichment * 100;
break;
}
}
switch (HalfLifeSettings.NewlySynthesizedTracerQuantity)
{
case TracerQuantity.LabeledAminoAcid:
result.RawValue = rowData.TracerPercent/100;
break;
case TracerQuantity.UnlabeledPeptide:
if (rowData.Peaks.Count > 0)
{
result.RawValue = rowData.Peaks[0].Area/rowData.AreaUnderCurve;
}
break;
}
if (!result.CurrentPrecursorPool.HasValue)
{
if (rowData.TracerPercent == result.InitialPrecursorPool)
{
// In an experiment with no labeling, we don't want to reject this item.
// Even if we don't know the CurrentPrecursorPool, we do know that the turnover is 0
result.Turnover = 0;
}
else
{
result.RejectReason = RejectReason.NoPrecursorPool;
return result;
}
}
else
{
switch (HalfLifeSettings.NewlySynthesizedTracerQuantity)
{
case TracerQuantity.PartialLabelDistribution:
{
var turnoverCalculator = GetTurnoverCalculator(rowData.Peptide.Sequence);
double? turnover;
double? turnoverScore;
turnoverCalculator.ComputeTurnover(result.CurrentPrecursorPool.Value, turnoverCalculator.ToTracerFormulaDict(rowData.PeakAreas), out turnover, out turnoverScore);
result.Turnover = turnover;
result.TurnoverScore = turnoverScore;
}
break;
case TracerQuantity.LabeledAminoAcid:
result.Turnover = (100 * result.RawValue - result.InitialPrecursorPool) /
(result.CurrentPrecursorPool - result.InitialPrecursorPool);
break;
case TracerQuantity.UnlabeledPeptide:
{
var turnoverCalculator = GetTurnoverCalculator(rowData.Peptide.Sequence);
var initialRawValue = turnoverCalculator.ExpectedUnlabeledFraction(result.InitialPrecursorPool);
var finalRawValue = turnoverCalculator.ExpectedUnlabeledFraction(result.CurrentPrecursorPool.Value);
result.Turnover = (result.RawValue - initialRawValue) / (finalRawValue - initialRawValue);
}
break;
}
if (null == result.RejectReason && ValidationStatus.accept != result.RawRowData.ValidationStatus)
{
if (0 < MinTurnoverScore && result.TurnoverScore < MinTurnoverScore)
{
result.RejectReason = RejectReason.LowTurnoverScore;
}
}
}
if (null == result.RejectReason && !result.Turnover.HasValue)
{
result.RejectReason = RejectReason.ValueOutOfRange;
}
return result;
}
