Exemplo n.º 1
0
        public static TMatrix StandardizeGToCreateX <TMatrix>(int maxValue, Matrix <string, string, double> gMatrix,
                                                              MatrixFactoryDelegate <TMatrix, string, string, double> zeroMatrixFractory,
                                                              ParallelOptions parallelOptions, bool onlyMeanCenter = false) where TMatrix : Matrix <string, string, double>
        {
            Console.WriteLine("StandardizeGToCreateX");
            //var xMatrix = DenseMatrix<string, string, double>.CreateDefaultInstance(gMatrix.RowKeys, gMatrix.ColKeys, double.NaN); //Inits to 0
            TMatrix xMatrix = zeroMatrixFractory(gMatrix.RowKeys, gMatrix.ColKeys, double.NaN);  //Inits to 0

            Helper.CheckCondition(xMatrix.GetValueOrMissing(0, 0) == 0, "xMatrix must start init'ed to zeros, but even at xMatrix[0,0] it is not 0");
            //First create x matrix
            //Parallel.ForEach(gMatrix.RowKeys, parallelOptions, var =>
            var counterWithMessages = new CounterWithMessages("StandardizeGToCreateX: row #{0}", 100, gMatrix.RowCount);

            foreach (string var in gMatrix.RowKeys)
            {
                counterWithMessages.Increment();

                //The paper divides by (2+2*Count) because its values are 0,1,2. Because ours are 0,1, we divide by (2+Count)
                var           row = gMatrix.SelectRowsView(var);
                List <double> nonMissingValues = row.Values.ToList();
                double        rowSum           = nonMissingValues.Sum();
                double        rowMean          = rowSum / (double)nonMissingValues.Count;
                double        piSmoothedCount  = (1.0 + rowSum)
                                                 / (2.0 + maxValue * (double)nonMissingValues.Count);
                double stdDevPi = Math.Sqrt(piSmoothedCount * (1 - piSmoothedCount));
                Helper.CheckCondition(!double.IsNaN(stdDevPi), "stdDevPi is NaN outside loop, likely because data input was not in 0/1/2 format as expected");

                Parallel.ForEach(row.RowKeyColKeyValues, parallelOptions, triple =>
                {
                    string cid    = triple.ColKey;
                    double gValue = triple.Value;
                    double xValue;
                    if (onlyMeanCenter)
                    {
                        xValue = (gValue - rowMean);
                    }
                    else
                    {
                        xValue = (gValue - rowMean) / stdDevPi;
                    }

                    xMatrix[var, cid] = xValue;
                    //if (doubleUp)
                    //{
                    //    xMatrix[new Pair<string, bool>(var, true), cid] = -xValue;
                    //}
                });
                //});
            }
            Console.WriteLine();
            return(xMatrix);
        }
Exemplo n.º 2
0
        static public TMatrix Standardize <TMatrix>(this TMatrix matrix, int maxMatrixVal, MatrixFactoryDelegate <TMatrix, string, string, double> zeroMatrixFractory, ParallelOptions parallelOptions) where TMatrix : Matrix <string, string, double>
        {
            TMatrix snpMatrixNew = EigenstratMain.StandardizeGToCreateX(maxMatrixVal, matrix, zeroMatrixFractory, parallelOptions);

            return(snpMatrixNew);
        }