private static List <PsmTsvLine> AssignFDRToTarget(string[] primaryLines, string[] secondaryLines)
{
List <PsmTsvLine> primaryPsms = ImportPsmtsv.ImportLinesToAggregate(primaryLines);
List <PsmTsvLine> secondaryPsms = ImportPsmtsv.ImportLinesToAggregate(secondaryLines);
primaryPsms = primaryPsms.OrderByDescending(x => x.score).ToList();
secondaryPsms = secondaryPsms.OrderByDescending(x => x.score).ToList();
int p = 0;
int s = 0;
int target = 0;
int decoy = 0;
double qMax = 0;
PsmTsvLine decoyLine = secondaryPsms[s];
while (p < primaryPsms.Count)
{
PsmTsvLine targetLine = primaryPsms[p];
if (targetLine.score > decoyLine.score || s == secondaryPsms.Count)
{
target++;
targetLine.target = target.ToString();
targetLine.decoy = decoy.ToString();
double qValue = (1.0d * decoy / target);
qMax = (qMax > qValue) ? qMax : qValue;
targetLine.q = qMax.ToString();
p++;
}
else
{
decoy++;
s++;
}
}
return(primaryPsms);
}
private static List <PsmTsvLine> AggregateDifferentDatabaseSearches(string[] primaryLines, string[] secondaryLines)
{
List <PsmTsvLine> primaryPsms = ImportPsmtsv.ImportLinesToAggregate(primaryLines);
List <PsmTsvLine> secondaryPsms = ImportPsmtsv.ImportLinesToAggregate(secondaryLines);
List <PsmTsvLine> aggregatedLines = new List <PsmTsvLine>();
int p = 0;
int s = 0;
while (p < primaryPsms.Count && s < secondaryPsms.Count)
{
PsmTsvLine psmP = primaryPsms[p];
PsmTsvLine psmS = secondaryPsms[s];
if (psmP.scanNumber < psmS.scanNumber)
{
aggregatedLines.Add(psmP);
p++;
}
else if (psmP.scanNumber > psmS.scanNumber)
{
aggregatedLines.Add(psmS);
s++;
}
else
{
if (psmP.score > psmS.score - 0.001 && psmP.score < psmS.score + 0.001)
{
aggregatedLines.Add(psmP.AggregateLine(psmS));
}
else if (psmP.score > psmS.score)
{
aggregatedLines.Add(psmP);
}
else
{
aggregatedLines.Add(psmS);
}
p++;
s++;
}
}
while (p < primaryPsms.Count)
{
aggregatedLines.Add(primaryPsms[p]);
p++;
}
while (s < secondaryPsms.Count)
{
aggregatedLines.Add(primaryPsms[s]);
s++;
}
return(aggregatedLines);
}
public static void RecursiveNeoAggregation(string standardFilePath, string neoResultFilePath, string outputFolder, string identifier)
{
//This method determines the optimum cutoff for gold standard identification and the minimum score difference required for a splice to outscore a normal
double qThreshold = 0;
double oldQThreshold = 0;
double scoreDifferenceThreshold = 0;
double oldScoreDifferenceThreshold = 0;
int numSplicedHighScoreQ = -1; //highest number of splice assignments at a 1% local FDR
int numSplicedHighScoreThreshold = -1; //highest number of splice assignments at a 1% local FDR
int numSplicedScore = 0; //current number of splic assignments at a 1% local FDR
bool increaseQ = true;
bool increaseScoreDifference = true;
string[] primaryLines = (System.IO.File.ReadAllLines(@standardFilePath));
string[] secondaryLines = (System.IO.File.ReadAllLines(@neoResultFilePath));
List <PsmTsvLine> primaryPsms = ImportPsmtsv.ImportLinesToAggregate(primaryLines);
primaryPsms.ForEach(x => x.neoType = PsmTsvLine.NeoType.Normal);
List <PsmTsvLine> secondaryPsms = ImportPsmtsv.ImportLinesToAggregate(secondaryLines);
do //determine if score difference should be changed
{
if (numSplicedScore <= numSplicedHighScoreThreshold) //check second time around if move score Threhold the other way
{
increaseScoreDifference = false;
}
else
{
numSplicedHighScoreThreshold = numSplicedScore; //update highscore
oldScoreDifferenceThreshold = scoreDifferenceThreshold; //update score difference
}
scoreDifferenceThreshold = UpdateScoreDifferenceThreshold(scoreDifferenceThreshold, increaseScoreDifference); //update score Threshold
do //determine gold standards to use
{
if (numSplicedScore <= numSplicedHighScoreQ) //check second time around if move qValue the other way
{
increaseQ = false;
}
else
{
numSplicedHighScoreQ = numSplicedScore; //update highscore
oldQThreshold = qThreshold; //updateQ
}
qThreshold = UpdateQThreshold(primaryPsms, qThreshold, increaseQ); //get qValue
List <PsmTsvLine> aggregatedLines = Percolate(primaryPsms, secondaryPsms, qThreshold, scoreDifferenceThreshold);
numSplicedScore = CalculateNumberOfConfidentSpliced(aggregatedLines);
} while (numSplicedScore > numSplicedHighScoreQ || increaseQ); //do again the otherway if done increasing
List <PsmTsvLine> oldAggregatedLines = Percolate(primaryPsms, secondaryPsms, oldQThreshold, scoreDifferenceThreshold);
numSplicedScore = CalculateNumberOfConfidentSpliced(oldAggregatedLines);
increaseQ = true;
qThreshold = oldQThreshold;
} while (numSplicedScore > numSplicedHighScoreThreshold || increaseScoreDifference);
List <PsmTsvLine> finalAggregatedLines = Percolate(primaryPsms, secondaryPsms, oldQThreshold, oldScoreDifferenceThreshold);
using (StreamWriter file = new StreamWriter(Path.Combine(outputFolder, identifier)))
{
file.WriteLine(primaryLines[0]); //header
foreach (PsmTsvLine line in finalAggregatedLines)
{
file.WriteLine(line.ToString());
}
}
using (StreamWriter file = new StreamWriter(Path.Combine(outputFolder, "PercolatorInfo_" + identifier)))
{
file.WriteLine("Maxmimum q-Value of Gold Standards: " + oldQThreshold);
file.WriteLine("Minimum Score Difference for Splice Selection Over Normal: " + oldScoreDifferenceThreshold);
}
}