public double GetQScorePredictor(QScorePredictor predictorId)
{
switch (predictorId)
{
case QScorePredictor.BinCount:
return((double)this.BinCount);
case QScorePredictor.LogBinCount:
return(Math.Log10(1 + this.BinCount));
case QScorePredictor.BinCountAmpDistance:
return(this.CopyNumber >= 15 ? Math.Log10(1 + this.BinCount) : 0.0);
case QScorePredictor.BinMean:
if (this.Counts.Count == 0)
{
return(0);
}
return(this.Counts.Average());
case QScorePredictor.BinCv:
if (this.Counts.Count == 0)
{
return(0);
}
if (this.Counts.Average() == 0)
{
return(0);
}
return(Utilities.CoefficientOfVariation(this.Counts));
case QScorePredictor.MafCount:
return(Alleles.Frequencies.Count);
case QScorePredictor.MafMean:
if (Alleles.Frequencies.Count == 0)
{
return(0);
}
return(Alleles.Frequencies.Average());
case QScorePredictor.MafCv:
if (Alleles.Frequencies.Count == 0)
{
return(0);
}
if (Alleles.Frequencies.Average() == 0)
{
return(0);
}
return(Utilities.CoefficientOfVariation(Alleles.Frequencies));
case QScorePredictor.LogMafCv:
return(Math.Log10(1 + GetQScorePredictor(QScorePredictor.MafCv)));
case QScorePredictor.ModelDistance:
return(this.ModelDistance);
case QScorePredictor.RunnerUpModelDistance:
return(this.RunnerUpModelDistance);
case QScorePredictor.DistanceRatio:
if (this.RunnerUpModelDistance == 0)
{
return(0);
}
return(this.ModelDistance / this.RunnerUpModelDistance);
case QScorePredictor.CopyNumber:
return((double)this.CopyNumber);
case QScorePredictor.MajorChromosomeCount:
// Force a double:
if (!this.MajorChromosomeCount.HasValue)
{
return(Math.Ceiling(this.CopyNumber / 2f));
}
return((double)this.MajorChromosomeCount);
}
return(0);
}
public double GetQScorePredictor(QScorePredictor predictorId)
{
switch (predictorId)
{
case QScorePredictor.BinCount:
return((double)this.BinCount);
case QScorePredictor.LogBinCount:
return(Math.Log10(1 + this.BinCount));
case QScorePredictor.BinCountAmpDistance:
return(this.CopyNumber >= 15 ? Math.Log10(1 + this.BinCount) : 0.0);
case QScorePredictor.BinMean:
if (this.Counts.Count == 0)
{
return(0);
}
return(this.Counts.Average());
case QScorePredictor.BinCv:
if (this.Counts.Count == 0)
{
return(0);
}
if (this.Counts.Average() == 0)
{
return(0);
}
return(Utilities.CoefficientOfVariation(this.Counts));
case QScorePredictor.MafCount:
return(Balleles.Frequencies.Count);
case QScorePredictor.MafMean:
if (Balleles.Frequencies.Count == 0)
{
return(0);
}
return(Balleles.Frequencies.Average());
case QScorePredictor.MafCv:
if (Balleles.Frequencies.Count == 0)
{
return(0);
}
if (Balleles.Frequencies.Average() == 0)
{
return(0);
}
return(Utilities.CoefficientOfVariation(Balleles.Frequencies));
case QScorePredictor.LogMafCv:
return(Math.Log10(1 + GetQScorePredictor(QScorePredictor.MafCv)));
case QScorePredictor.ModelDistance:
// HACK: high copy number needs some help: higher variance and general lack of interest in exact copy number
return(this.ModelDistance / Math.Max(1.0, this.CopyNumber - 4.0));
case QScorePredictor.RunnerUpModelDistance:
return(this.RunnerUpModelDistance);
case QScorePredictor.DistanceRatio:
if (this.RunnerUpModelDistance == 0)
{
return(0);
}
return(this.ModelDistance / this.RunnerUpModelDistance);
case QScorePredictor.CopyNumber:
return((double)this.CopyNumber);
case QScorePredictor.MajorChromosomeCount:
// Force a double:
if (!this.MajorChromosomeCount.HasValue)
{
return(Math.Ceiling(this.CopyNumber / 2f));
}
return((double)this.MajorChromosomeCount);
}
return(0);
}
public double GetQScorePredictor(QScorePredictor predictorId)
{
switch (predictorId)
{
case QScorePredictor.BinCount:
return (double)this.BinCount;
case QScorePredictor.LogBinCount:
return Math.Log10(1 + this.BinCount);
case QScorePredictor.BinMean:
if (this.Counts.Count == 0) return 0;
return this.Counts.Average();
case QScorePredictor.BinCv:
if (this.Counts.Count == 0) return 0;
if (this.Counts.Average() == 0) return 0;
return CanvasCommon.Utilities.CoefficientOfVariation(this.Counts);
case QScorePredictor.MafCount:
return this.VariantFrequencies.Count;
case QScorePredictor.MafMean:
if (this.VariantFrequencies.Count == 0) return 0;
return this.VariantFrequencies.Average();
case QScorePredictor.MafCv:
if (this.VariantFrequencies.Count == 0) return 0;
if (this.VariantFrequencies.Average() == 0) return 0;
return CanvasCommon.Utilities.CoefficientOfVariation(this.VariantFrequencies);
case QScorePredictor.LogMafCv:
return Math.Log10(1 + GetQScorePredictor(QScorePredictor.MafCv));
case QScorePredictor.ModelDistance:
return this.ModelDistance;
case QScorePredictor.RunnerUpModelDistance:
return this.RunnerUpModelDistance;
case QScorePredictor.DistanceRatio:
if (this.RunnerUpModelDistance == 0) return 0;
return this.ModelDistance / this.RunnerUpModelDistance;
case QScorePredictor.CopyNumber:
return (double)this.CopyNumber;
case QScorePredictor.MajorChromosomeCount:
// Force a double:
if (!this.MajorChromosomeCount.HasValue) return Math.Ceiling(this.CopyNumber / 2f);
return (double)this.MajorChromosomeCount;
}
return 0;
}
