private void ConfirmPeak(Peak p, List <AnalysisResult <Peak, Metadata> .SupportingPeak> supportingPeaks)
{
var anRe = new AnalysisResult <Peak, Metadata> .ProcessedPeak()
{
peak = p,
xSquared = tXsqrd,
rtp = ChiSquaredCache.ChiSqrdDistRTP(tXsqrd, 2 + (supportingPeaks.Count * 2)),
supportingPeaks = supportingPeaks
};
if (p.metadata.value <= Options.tauS)
{
analysisResults.R_j___sc[chrTitle]++;
anRe.classification = PeakClassificationType.StringentConfirmed;
}
else
{
analysisResults.R_j___wc[chrTitle]++;
anRe.classification = PeakClassificationType.WeakConfirmed;
}
if (!analysisResults.R_j__c[chrTitle].ContainsKey(p.metadata.hashKey))
{
analysisResults.R_j__c[chrTitle].Add(p.metadata.hashKey, anRe);
}
ConfirmeSupportingPeaks(p, supportingPeaks);
}
private void DiscardSupportingPeaks(Peak p, List <AnalysisResult <Peak, Metadata> .SupportingPeak> supportingPeaks, byte discardReason)
{
foreach (var supPeak in supportingPeaks)
{
if (!Data <Peak, Metadata> .analysisResults[supPeak.sampleIndex].R_j__d[chrTitle].ContainsKey(supPeak.peak.metadata.hashKey))
{
var tSupPeak = new List <AnalysisResult <Peak, Metadata> .SupportingPeak>();
var targetSample = Data <Peak, Metadata> .analysisResults[supPeak.sampleIndex];
tSupPeak.Add(new AnalysisResult <Peak, Metadata> .SupportingPeak()
{
peak = p, sampleIndex = sampleHashKey
});
foreach (var sP in supportingPeaks)
{
if (supPeak.CompareTo(sP) != 0)
{
tSupPeak.Add(sP);
}
}
var anRe = new AnalysisResult <Peak, Metadata> .ProcessedPeak()
{
peak = supPeak.peak,
xSquared = tXsqrd,
reason = discardReason,
rtp = ChiSquaredCache.ChiSqrdDistRTP(tXsqrd, 2 + (supportingPeaks.Count * 2)),
supportingPeaks = tSupPeak
};
if (supPeak.peak.metadata.value <= Options.tauS)
{
targetSample.R_j__sdt[chrTitle]++;
anRe.classification = PeakClassificationType.StringentDiscarded;
}
else
{
targetSample.R_j__wdt[chrTitle]++;
anRe.classification = PeakClassificationType.WeakDiscarded;
}
targetSample.R_j__d[chrTitle].Add(supPeak.peak.metadata.hashKey, anRe);
}
}
}
public void Run(AnalysisOptions options)
{
Options.replicateType = options.replicateType;
Options.C = options.C;
Options.tauS = options.tauS;
Options.tauW = options.tauW;
Options.gamma = options.gamma;
Options.alpha = options.alpha;
Options.multipleIntersections = options.multipleIntersections;
Data <Peak, Metadata> .cachedChiSqrd = new List <double>();
for (int i = 1; i <= Data <Peak, Metadata> .sampleKeys.Count; i++)
{
Data <Peak, Metadata> .cachedChiSqrd.Add(Math.Round(ChiSquaredCache.ChiSqrdINVRTP(Options.gamma, (byte)(i * 2)), 3));
}
Data <Peak, Metadata> .BuildSharedItems();
processor = new Processor <Peak, Metadata>();
#region .::. Status .::.
int totalSteps = Data <Peak, Metadata> .sampleKeys.Count + 3;
int stepCounter = 0;
#endregion
Console.WriteLine("");
foreach (var sampleKey in Data <Peak, Metadata> .sampleKeys)
{
var sample = Samples <Peak, Metadata> .Data[sampleKey.Key];
#region .::. Status .::.
if (sampleKey.Value.Length > 36)
{
Console.Write("\r[" + (++stepCounter).ToString() + "\\" + totalSteps + "] processing sample: ..." + sampleKey.Value.Substring(sampleKey.Value.Length - 35, 35));
}
else
{
Console.Write("\r[" + (++stepCounter).ToString() + "\\" + totalSteps + "] processing sample: " + sampleKey.Value);
}
Console.WriteLine("");
#endregion
foreach (var chr in sample.intervals)
{
foreach (var strand in chr.Value)
{
int currentLineCursor = Console.CursorTop;
Console.SetCursorPosition(0, Console.CursorTop);
Console.Write(new string(' ', Console.WindowWidth));
Console.SetCursorPosition(0, currentLineCursor);
Console.Write("\r .::. Processing {0}", chr.Key);
processor.Run(sampleKey.Key, chr.Key, strand.Key);
}
}
}
#region .::. Status .::.
Console.Write("\r[" + (++stepCounter).ToString() + "\\" + totalSteps + "] Purifying intermediate sets.");
#endregion
processor.IntermediateSetsPurification();
#region .::. Status .::.
Console.WriteLine("[" + (++stepCounter).ToString() + "\\" + totalSteps + "] Creating output set.");
#endregion
processor.CreateOuputSet();
#region .::. Status .::.
Console.WriteLine("[" + stepCounter + "\\" + totalSteps + "] Performing Multiple testing correction.");
#endregion
processor.EstimateFalseDiscoveryRate();
}