source: trunk/yat/normalization/QuantileNormalizer.cc @ 1432

// $Id: QuantileNormalizer.cc 1432 2008-08-25 13:54:18Z peter $

/*
  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
  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 2 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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
  02111-1307, USA.
*/

#include "QuantileNormalizer.h"

#include "yat/statistics/Averager.h"

#include "yat/utility/Matrix.h"
#include "yat/utility/VectorConstView.h"

namespace theplu {
namespace yat {
namespace normalization {

  void QuantileNormalizer::operator()(utility::Matrix& data) const
  {
    utility::Matrix data_copy(data);
    
    // sort columns in copy
    for (size_t column=0; column<data_copy.columns(); ++column){
      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
    }

    // calculate average of each row
    std::vector<yat::statistics::Averager> averager(data_copy.rows());
    for (size_t row=0; row<data_copy.rows(); ++row){
      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
    }

    for (size_t column=0; column<data.columns(); ++column){
      std::vector<size_t> index;
      utility::sort_index(index, data.column_const_view(column));
                               
      for (size_t row=0; row<data.rows(); ++row)
        data(index[row], column) = averager[row].mean();
    }
  }



}}} // end of namespace utility, yat and thep