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);
}
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);
}