source: trunk/yat/normalization/QuantileNormalizer.cc @ 1453

Last change on this file since 1453 was 1453, checked in by Peter, 13 years ago

some docs

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1// $Id: QuantileNormalizer.cc 1453 2008-08-29 15:41:09Z 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
33#include <cassert>
34
35namespace theplu {
36namespace yat {
37namespace normalization {
38
39  void QuantileNormalizer::operator()(const utility::Matrix& data,
40                                      utility::Matrix& result) const
41  {
42    assert(data.rows()==result.rows());
43    utility::Matrix data_copy(data);
44   
45    // sort columns in copy
46    for (size_t column=0; column<data_copy.columns(); ++column){
47      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
48    }
49
50    // calculate average of each row
51    std::vector<yat::statistics::Averager> averager(data_copy.rows());
52    for (size_t row=0; row<data_copy.rows(); ++row){
53      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
54    }
55
56    for (size_t column=0; column<result.columns(); ++column){
57      std::vector<size_t> index;
58      utility::sort_index(index, result.column_const_view(column));
59                               
60      for (size_t row=0; row<result.rows(); ++row)
61        result(index[row], column) = averager[row].mean();
62    }
63  }
64
65
66
67}}} // end of namespace utility, yat and thep
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