public FdrResult FilterByFdr(double maxFdr)
{
if (this.Count == 0)
{
return(new FdrResult());
}
this.ForEach(m => m.FilterByFdr(maxFdr));
if (OverlapBySearchEngine.Count == 0)
{
return(new FdrResult()
{
Fdr = maxFdr, Spectra = this.GetUnconflictedOptimalSpectra()
});
}
double nextFdr = maxFdr;
while (true)
{
FdrResult result = DoCalculateOverlappedPeptideFdr(nextFdr);
if (result.Fdr <= maxFdr)
{
return(result);
}
nextFdr = nextFdr - FalseDiscoveryRateUtils.CalculateStepFdr(nextFdr);
this.ForEach(m => m.FilterByFdr(nextFdr));
}
}
private FdrResult DoCalculateOverlappedPeptideFdr(double individualFdr)
{
FdrResult result = new FdrResult();
List <IIdentifiedSpectrum> spectra = new List <IIdentifiedSpectrum>();
int decoyCount = 0;
int targetCount = 0;
foreach (var dsList in OverlapBySearchEngine)
{
List <IIdentifiedSpectrum> peps = dsList.GetUnconflictedOptimalSpectra();
//根据实验文件名分类。这样可以降低需要比较的集合大小。
var expGroups = peps.GroupBy(m => m.Query.FileScan.Experimental);
foreach (var group in expGroups)
{
//根据scan分类。
var spGroup = group.GroupBy(m => m.Query.FileScan.FirstScan);
foreach (var sp in spGroup)
{
var lst = sp.ToList();
if (lst.Count > 1 && IsEngineConflict(lst))
{
result.ConflictSpectra.AddRange(lst);
var spectrum = conflictFunc.Process(lst);
lst.Clear();
if (spectrum != null)
{
lst.AddRange(spectrum);
}
}
if (lst.Count >= dsOptions.Options.MinimumEngineAgreeCount)
{
spectra.AddRange(lst);
if (lst[0].FromDecoy)
{
decoyCount++;
}
else
{
targetCount++;
}
}
}
}
}
if (dsOptions.Options.MinimumEngineAgreeCount <= 1)
{
var noOverlapSpectra = NoOverlaps.GetOptimalSpectra();
foreach (var s in noOverlapSpectra)
{
if (s.FromDecoy)
{
decoyCount++;
}
else
{
targetCount++;
}
}
spectra.AddRange(noOverlapSpectra);
}
result.Spectra = spectra;
result.Fdr = fdrCalc.Calculate(decoyCount, targetCount);
return(result);
}
