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

Last change on this file since 1432 was 1432, checked in by Peter, 13 years ago

refs #416 moving quantile normalizer to new dir. Also moved the algorithm to a class (rather than free function).

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 1.9 KB
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1// $Id: QuantileNormalizer.cc 1432 2008-08-25 13:54:18Z peter $
2
3/*
4  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
5  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
6  Copyright (C) 2008 Peter Johansson
7
8  This file is part of the yat library, http://dev.thep.lu.se/yat
9
10  The yat library is free software; you can redistribute it and/or
11  modify it under the terms of the GNU General Public License as
12  published by the Free Software Foundation; either version 2 of the
13  License, or (at your option) any later version.
14
15  The yat library is distributed in the hope that it will be useful,
16  but WITHOUT ANY WARRANTY; without even the implied warranty of
17  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18  General Public License for more details.
19
20  You should have received a copy of the GNU General Public License
21  along with this program; if not, write to the Free Software
22  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
23  02111-1307, USA.
24*/
25
26#include "QuantileNormalizer.h"
27
28#include "yat/statistics/Averager.h"
29
30#include "yat/utility/Matrix.h"
31#include "yat/utility/VectorConstView.h"
32
33namespace theplu {
34namespace yat {
35namespace normalization {
36
37  void QuantileNormalizer::operator()(utility::Matrix& data) const
38  {
39    utility::Matrix data_copy(data);
40   
41    // sort columns in copy
42    for (size_t column=0; column<data_copy.columns(); ++column){
43      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
44    }
45
46    // calculate average of each row
47    std::vector<yat::statistics::Averager> averager(data_copy.rows());
48    for (size_t row=0; row<data_copy.rows(); ++row){
49      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
50    }
51
52    for (size_t column=0; column<data.columns(); ++column){
53      std::vector<size_t> index;
54      utility::sort_index(index, data.column_const_view(column));
55                               
56      for (size_t row=0; row<data.rows(); ++row)
57        data(index[row], column) = averager[row].mean();
58    }
59  }
60
61
62
63}}} // end of namespace utility, yat and thep
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