CanvasDiploidCaller.CanvasDiploidCaller.AssignPloidyCallsGaussianMixture C# (CSharp) Метод

        void AssignPloidyCallsGaussianMixture()
        {
            // For segments with (almost) no variants alleles at all, we'll assign them a dummy MAF, and
            // we simply won't consider MAF when determining the closest ploidy:
            double dummyMAF = -1;

            foreach (CanvasSegment segment in this.Segments)
            {
                // Compute (MAF, Coverage) for this segment:
                List<double> MAF = new List<double>();
                foreach (float VF in segment.VariantFrequencies) MAF.Add(VF > 0.5 ? 1 - VF : VF);
                double medianCoverage = CanvasCommon.Utilities.Median(segment.Counts);
                double medianMAF = dummyMAF;

                SegmentPloidy bestPloidy = null;
                double bestProbability = 0;

                if (MAF.Count >= 10)
                {
                    medianMAF = Utilities.Median(MAF);
                }

                Dictionary<SegmentPloidy, double> posteriorProbabilities = GaussianMixtureModel.EMComputePosteriorProbs(AllPloidies, medianMAF, medianCoverage);
                // Find the closest ploidy.
                foreach (SegmentPloidy ploidy in AllPloidies)
                {
                    if (bestPloidy == null || posteriorProbabilities[ploidy] > bestProbability)
                    {
                        bestProbability = posteriorProbabilities[ploidy];
                        bestPloidy = ploidy;
                    }
                }

                if (bestProbability == 0)
                {
                    // Sanity-check: If we didn't find anything with probability > 0, then fall back to the simplest possible
                    // thing: Call purely on coverage.
                    segment.CopyNumber = (int)Math.Round(2 * medianCoverage / this.DiploidCoverage);
                    segment.MajorChromosomeCount = null;
                }
                else
                {
                    segment.CopyNumber = bestPloidy.CopyNumber;
                    segment.MajorChromosomeCount = bestPloidy.MajorChromosomeCount;
                    if (MAF.Count < 10) segment.MajorChromosomeCount = null; // Don't assign MCC if we don't have variant allele frequencies
                }
            }
        }