public void CalculateRatio(SrmOptions options)
{
if (this.IsPaired)
{
CalculateRatioAndArea(options.DeductBaseLine);
if (options.RatioByArea)
{
this.Ratio = this.LightArea / this.HeavyArea;
}
}
}
protected override IFileProcessor GetFileProcessor()
{
SrmOptions options = new SrmOptions()
{
DistillerSoftware = this.Text,
AskForSmooth = smooth.Checked,
DeductBaseLine = deductBaseLine.Checked,
RangeSelectionByNoise = peakPickingByBaseline.Checked,
ValidationMinSignalToNoise = validateSignalToNoise.Value,
ValidationMinRegressionCorrelation = validateCorrel.Value,
MzTolerance = mzTolerance.Value,
MinValidTransitionPair = minValidTransactionPair.Value,
//MinRetentionWindowInMinute = 0,
MinEnabledScan = minEnabledScan.Value,
HasDecoy = hasDecoy.Checked,
DecoyPattern = decoyPattern.Text,
RatioByArea = cbRatioByArea.Checked,
RefineData = cbRefinePeakPicking.Checked
};
if (peakPickingByBaseline.Checked)
{
options.MinPeakPickingSignalToNoise = signalToNoise.Value;
options.LowestPercentageForNoise = baseLinePercentage.Value / 100;
}
else
{
options.PercentageOfHighestPeak = highestPeakPercentage.Value / 100;
}
if (clusterByPredefine.Checked)
{
options.DefinitionFile = predefinedFile.FullName;
options.DefinitionFileFormat = formats.SelectedItem.GetName();
}
else
{
options.PrecursorMassDistance = ParseGaps();
options.RetentionTimeToleranceInSecond = rtToleranceInSecond.Value;
}
options.RawFiles = dataDirs.SelectPathMap;
options.ToXml(true).Save(this.GetOriginFile());
return(new SrmDistiller());
}
public SrmPairedResult()
{
Options = new SrmOptions();
Modified = false;
}
public override IEnumerable <string> Process(string optionFile)
{
var targetDirectory = Path.GetDirectoryName(optionFile);
options = new SrmOptions();
options.FromXml(XElement.Load(optionFile));
var keys = options.RawFiles.Keys.ToList();
foreach (var key in keys)
{
if (string.IsNullOrEmpty(options.RawFiles[key]))
{
this.options.RawFiles[key] = key;
}
}
List <string> result = new List <string>();
bool ignoreWarning = false;
Dictionary <string, List <string> > map = GetGroupMap();
int totalCount = options.RawFiles.Count;
int curIndex = 0;
foreach (var groupKey in map.Keys)
{
var mrmFile = GetMrmFileName(targetDirectory, groupKey);
SrmPairedResult taskResult = new SrmPairedResult()
{
Options = this.options
};
var files = map[groupKey];
foreach (var rawFile in files)
{
curIndex++;
this.prefix = MyConvert.Format("Processing {0}/{1}", curIndex, totalCount);
SetProgressMessage(rawFile);
Console.WriteLine(rawFile);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
//读取所有scan信息
List <SrmScan> mrmIntensities = GetMRMScans(rawFile);
//mrmIntensities.RemoveAll(m => !( Math.Abs(m.PrecursorMz - 767.4) < 0.1 || Math.Abs(m.PrecursorMz - 770.9) < 0.1));
SetProgressMessage("building mrm groups ...");
var mrms = ScanToTransaction(mrmIntensities);
//将MRMPeptideItem转换为MRMPairedPeptideItem对象
SrmPairedResult mrmPairs;
if (File.Exists(options.DefinitionFile))
{
mrmPairs = BuildResultBasedOnDefinedFile(ref ignoreWarning, mrms);
}
else
{
mrmPairs = BuildResultBasedOnRealData(mrms);
}
mrmPairs.Options = this.options;
mrmPairs.PeakPicking();
//固定阈值筛选。
var filter = mrmPairs.Options.GetFilter();
mrmPairs.ForEach(m =>
{
m.ProductIonPairs.ForEach(n => n.Enabled = filter.Accept(n));
});
taskResult.AddRange(mrmPairs);
}
if (options.HasDecoy)
{
//设置decoy标签
taskResult.AssignDecoy();
//是否有真实的decoy transition
var hasDecoy = taskResult.Any(m => m.ProductIonPairs.Any(n => n.IsDecoy));
if (hasDecoy)
{
//选取所有transition pairs，这些transition pairs有线性回归比值和回归系数
var pairs = (from m in taskResult
from n in m.ProductIonPairs
where n.IsPaired && n.Enabled
orderby n.RegressionCorrelation descending
select n).ToList();
//如果有这些pair，那么，那些不成pair的transition全部设置为disabled
if (pairs.Count > 0)
{
taskResult.ForEach(m => m.ProductIonPairs.ForEach(n => n.Enabled = n.Enabled && n.IsPaired));
}
//计算每个pair的qvalue
TargetFalseDiscoveryRateCalculator calc = new TargetFalseDiscoveryRateCalculator();
var decoyCount = pairs.Count(m => m.IsDecoy);
var targetCount = pairs.Count - decoyCount;
for (int d = pairs.Count - 1; d >= 0; d--)
{
pairs[d].Qvalue = calc.Calculate(decoyCount, targetCount);
if (pairs[d].IsDecoy)
{
decoyCount--;
}
else
{
targetCount--;
}
}
//找到qvalue小于给定fdr的pair，qvalue大于该pair的全部设置为disable
for (int d = pairs.Count - 1; d >= 0; d--)
{
if (!pairs[d].IsDecoy && pairs[d].Qvalue <= options.TransitionFdr)
{
for (int d2 = d + 1; d2 < pairs.Count - 1; d2++)
{
pairs[d2].Enabled = false;
}
break;
}
}
}
}
taskResult.ForEach(m =>
{
m.CheckEnabled(this.options.OutlierEvalue, this.options.MinValidTransitionPair);
});
taskResult.CalculatePeptideRatio();
taskResult.Sort((m1, m2) => m1.LightPrecursorMZ.CompareTo(m2.LightPrecursorMZ));
new SrmPairedResultXmlFormat().WriteToFile(mrmFile, taskResult);
result.Add(mrmFile);
}
Progress.End();
return(result);
}
/// <summary>
/// 根据给定算法进行区间选择
/// </summary>
/// <param name="peakPicking">区间选择算法</param>
/// <param name="deductBaseLine">是否需要去除基线</param>
public void PeakPicking(IRangeSelection peakPicking, SrmOptions options)
{
//首先，每个独立进行peakpicking。
foreach (var product in ProductIonPairs)
{
product.PeakPicking(peakPicking);
product.CalculateRatio(options);
product.Enabled = false;
}
if (options.RefineData && ProductIonPairs.Count > 1)
{
//如果所有scan都是false，直接返回。
if (!ProductIonPairs.Any(m => m.EnabledScanCount > 0))
{
return;
}
int maxIndex;
if (IsPaired)
{
//选择correlation最高的一个作为标准
var maxCorr = double.MinValue;
maxIndex = -1;
for (int i = 0; i < ProductIonPairs.Count; i++)
{
if (ProductIonPairs[i].EnabledScanCount == 0)
{
continue;
}
if (maxCorr < ProductIonPairs[i].RegressionCorrelation)
{
maxCorr = ProductIonPairs[i].RegressionCorrelation;
maxIndex = i;
}
}
}
else//只有轻标结果
{
var maxIntensity = 0.0;
maxIndex = 0;
for (int i = 0; i < ProductIonPairs.Count; i++)
{
var intensities = (from s in ProductIonPairs[i].Light.Intensities
where s.Enabled
select s.Intensity).ToList();
if (intensities.Count > 0)
{
var maxInt = intensities.Max();
if (maxIntensity < maxInt)
{
maxIntensity = maxInt;
maxIndex = i;
}
}
}
}
var rts = (from m in ProductIonPairs[maxIndex].Light.Intensities
where m.Enabled
orderby m.RetentionTime
select m.RetentionTime).ToList();
this.SetEnabledRetentionTimeRange(rts.First(), rts.Last());
}
this.CalculateTransactionRatio(options);
}
/// <summary>
/// 计算每个离子对的轻重比及面积
/// </summary>
/// <param name="deductBaseLine">是否去除基线。当去除基线时，结果为Light = a * Heavy，过原点。否则为Light = a * Heavy + b，b为截距。</param>
public void CalculateTransactionRatio(SrmOptions options)
{
this.ProductIonPairs.ForEach(m => m.CalculateRatio(options));
}
