source: trunk/yat/normalizer/QuantileNormalizer.h @ 1577

#ifndef _theplu_yat_normalizer_quantile_normalizer_
#define _theplu_yat_normalizer_quantile_normalizer_

// $Id: QuantileNormalizer.h 1577 2008-10-14 13:49:49Z peter $

/*
  Copyright (C) 2008 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

namespace theplu {
namespace yat {
namespace utility {
  class Matrix;
}
namespace normalizer {

  /**
     \brief Perform quantile normalization

     After a quantile normalization each column has the same
     distribution of data (the quantiles are the same). Also, within
     each column the rank of an element is not changed. The
     distribution that each column follows is determined by taking the
     average across columns, i.e., the largest element in each column
     will be equal to the average of the largest elements. The 2nd
     largest element in each column will be equal to the average of
     the 2nd largest element in eacc column et cetera.

     There is currently no weighted version of QuantileNormalizer

     \since New in yat 0.5
   */
  class QuantileNormalizer
  {
  public:
    /**
       \brief perform the quantile normalization.

       It is possible to normalize "in place"; it is permissible for
       \a matrix and \a result to reference to the same Matrix.

       \note dimensions of \a matrix and \a result must match.
     */
    void operator()(const utility::Matrix& matrix,
                    utility::Matrix& result) const;
  };

}}} // end of namespace normalizer, yat and thep
#endif