How is localSD metric calculated

[eroller]

        /// <summary>
        /// Estimate local standard deviation (SD).
        /// </summary>
        /// <param name="bins">Genomic bins from which we filter out local SD outliers associated with FFPE biases.</param>
        /// <param name="threshold">Median SD value which is used to determine whereas to run RemoveBinsWithExtremeLocalMad on a sample and which set of bins to remove (set as threshold*5).</param>
        /// The rationale of this function is that standard deviation of difference of consecutive bins values, when taken over a small range of bin (i.e. 20 bins),
        /// has a distinct distribution for FFPE compared to Fresh Frozen (FF) samples. This property is used to flag and remove such bins.

        static double getLocalStandardDeviation(List<GenomicBin> bins)
        {
            // Will hold consecutive bin count difference (approximates Skellam Distribution: mean centred on zero so agnostic to CN changes)
            double[] countsDiffs = new double[bins.Count - 1];

            for (int binIndex = 0; binIndex < bins.Count - 1; binIndex++)
            {
                countsDiffs[binIndex] = Convert.ToDouble(bins[binIndex + 1].Count - bins[binIndex].Count);
            }

            // holder of local SD values (SDs of 20 bins)
            List<double> localSDs = new List<double>();
            List<string> chromosomeBin = new List<string>();

            // calculate local SD metric
            int windowSize = 20;
            for (int windowEnd = windowSize, windowStart = 0; windowEnd < countsDiffs.Length; windowStart += windowSize, windowEnd += windowSize)
            {
                double localSD = Utilities.StandardDeviation(countsDiffs, windowStart, windowEnd);
                localSDs.Add(localSD);
                chromosomeBin.Add(bins[windowStart].Chromosome);
                for (int binIndex = windowStart; binIndex < windowEnd; binIndex += 1)
                {
                    bins[binIndex].MadOfDiffs = localSD;
                }
            }

            // average of local SD metric
            double localSDaverage = GetLocalStandardDeviationAverage(localSDs, chromosomeBin);
            return localSDaverage;
        }