public static FDRResult GenerateFDRStatistics(ProteinManager myProteins, Parameters myParams)
{
//Generate FDR statistics
Console.WriteLine("Unique Proteins--->" + myProteins.MyProteinList.Count);
PeptideAnalysisPckg p = new PeptideAnalysisPckg(myProteins.AllSQTScans, myParams);
Console.Write(p.GoodScans);
int labeledDecoyScans = p.BadScans.Count;
int labeledDecoyProteins = myProteins.MyProteinList.FindAll(a => a.Locus.StartsWith(myParams.LabeledDecoyTag)).Count;
FDRResult fdrResult = new FDRResult();
fdrResult.ReversedProteins = labeledDecoyProteins;
fdrResult.TotalProteins = myProteins.MyProteinList.Count;
fdrResult.ReversedPeptides = p.MyBadPeptideDic.Keys.Count;
fdrResult.TotalPeptides = p.MyBadPeptideDic.Keys.Count + p.MyGoodPeptideDic.Count;
fdrResult.ReversedSpectra = labeledDecoyScans;
fdrResult.TotalSpectra = myProteins.AllSQTScans.Count;
return(fdrResult);
}
public ResultPackage
(ProteinManager myProteins,
Parameters parameters,
string databaseUsed,
string sqtDirectory,
bool lockMass
)
{
this.lockMass = lockMass;
this.MyProteins = myProteins;
this.MyParameters = parameters;
this.Database = databaseUsed;
this.SQTDirectory = sqtDirectory;
this.MyFDRResult = FDRStatistics.GenerateFDRStatistics(myProteins, MyParameters);
}