private static Dictionary <string, Set <Hla> > ExtractPeptideToHlaSet(QmrrModelAllPeptides qmrrModel)
{
Dictionary <string, Set <Hla> > realPeptideToHlaSet = new Dictionary <string, Set <Hla> >();
foreach (string peptide in qmrrModel.BestParamsAndHlaAssignments.PeptideToBestHlaAssignmentSoFar.Keys)
{
realPeptideToHlaSet.Add(peptide, qmrrModel.BestParamsAndHlaAssignments.PeptideToBestHlaAssignmentSoFar[peptide].Champ.CreateHlaAssignmentAsSet());
}
return(realPeptideToHlaSet);
}
//private static OptimizationParameterList CreateQmrrParamsX(double causePrior, double leakProbability, Set<string> candidateHlaSet)
//{
// List<Parameter> parameterCollection = new List<Parameter>();
// parameterCollection.Add(Parameter.GetProbabilityInstance("causePrior", causePrior, false));
// foreach (string hla in candidateHlaSet)
// {
// if (hla == "B1599")
// {
// Parameter aParameter = Parameter.GetProbabilityInstance("link" + hla, 0, false);
// parameterCollection.Add(aParameter);
// }
// else
// {
// Parameter aParameter = Parameter.GetProbabilityInstance("link" + hla, .5, true);
// parameterCollection.Add(aParameter);
// }
// }
// parameterCollection.Add(Parameter.GetProbabilityInstance("leakProbability", leakProbability, false));
// parameterCollection.Add(Parameter.GetPositiveFactorInstance("useKnownList", 1, false));
// OptimizationParameterList qmrrParamsStart = OptimizationParameterList.GetInstance2(parameterCollection);
// return qmrrParamsStart;
//}
//private static Dictionary<string, string> LoadOriginalParameters(string directory)
//{
// string parameterFileName = string.Format(@"{0}\{1}", directory, "NoisyOr.Parameters.TwoCause.UseKnown.txt");//!!!const
// string header = "dataset varyFitFactor score causePrior fitFactor leakProbability link useKnownList";
// foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(parameterFileName, header, false))
// {
// bool varyFitFactor = bool.Parse(row["varyFitFactor"]);
// if (!varyFitFactor)
// {
// return row;
// }
// }
// Debug.Fail("Didn't find expected line");
// return null;
//}
//static Dictionary<string, Set<string>> LoadOriginalPeptideToHlaSet(string directory)
//{
// string fileName = string.Format(@"{0}\{1}", directory, @"NoisyOr.HlasPerPeptide.hivmodel.TwoCauseFalse.UseKnownTrue.txt");
// Dictionary<string, Set<string>> originalPeptideToHlaSet = new Dictionary<string, Set<string>>();
// string header = "Peptide HLAAssignment LogLikelihood";
// foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(fileName, header, false))
// {
// string peptide = row["Peptide"];
// Set<string> hlaSet = Set<string>.GetInstance(row["HLAAssignment"].Split(';'));
// originalPeptideToHlaSet.Add(peptide, hlaSet);
// }
// return originalPeptideToHlaSet;
//}
public static QmrrModelAllPeptides CreateSimpleModel(string directory, string casename, bool useKnownList)
{
OptimizationParameterList qmrrParamsStart = OptimizationParameterList.GetInstance(
OptimizationParameter.GetProbabilityInstance("causePrior", .01, true),
OptimizationParameter.GetProbabilityInstance("link", .5, true),
OptimizationParameter.GetProbabilityInstance("leakProbability", .003, true),
OptimizationParameter.GetPositiveFactorInstance("useKnownList", useKnownList ? 1 : 0, false)
);
ModelLikelihoodFactories modelLikelihoodFactories = ModelLikelihoodFactories.GetInstanceThreeParamSlow(qmrrParamsStart);
double depth = 1.5;
string dataset = string.Format(@"{0}\{1}", directory, casename);
QmrrModelAllPeptides qmrrModel = QmrrModelAllPeptides.GetInstance(modelLikelihoodFactories, dataset, qmrrParamsStart, depth, "noConstraints");
return(qmrrModel);
}
