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# Licensed to the Apache Software Foundation (ASF) under one
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# to you under the Apache License, Version 2.0 (the
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#
#   http://www.apache.org/licenses/LICENSE-2.0
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m_scale = function(Matrix[Double] X, Boolean center, Boolean scale) return (Matrix[Double] Y) {
  # This function centers scales and performs z-score on the input matrix X

  if( center )
    X = X - colMeans(X);

  if (scale) {
    N = nrow(X);
    if( center )
      cvars = (colSums(X^2) - N*(colMeans(X)^2))/(N-1);
    else
      cvars = colSums(X^2)/(N-1);

    #scale by std-dev and replace NaNs with 0's
    X = replace(target=X/sqrt(cvars),
      pattern=NaN, replacement=0);
  }
  Y = X;
}