source: trunk/yat/normalizer/QuantileNormalizer.h @ 1602

Last change on this file since 1602 was 1578, checked in by Peter, 13 years ago

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1#ifndef _theplu_yat_normalizer_quantile_normalizer_
2#define _theplu_yat_normalizer_quantile_normalizer_
3
4// $Id: QuantileNormalizer.h 1578 2008-10-14 19:01:02Z peter $
5
6/*
7  Copyright (C) 2008 Peter Johansson
8
9  This file is part of the yat library, http://dev.thep.lu.se/yat
10
11  The yat library is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License as
13  published by the Free Software Foundation; either version 3 of the
14  License, or (at your option) any later version.
15
16  The yat library is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19  General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with yat. If not, see <http://www.gnu.org/licenses/>.
23*/
24
25namespace theplu {
26namespace yat {
27namespace utility {
28  class Matrix;
29}
30namespace normalizer {
31
32  /**
33     \brief Perform quantile normalization
34
35     After a quantile normalization each column has the same
36     distribution of data (the quantiles are the same). Also, within
37     each column the rank of an element is not changed. The
38     distribution that each column follows is determined by taking the
39     average across columns, i.e., the largest element in each column
40     will be equal to the average of the largest elements. The 2nd
41     largest element in each column will be equal to the average of
42     the 2nd largest element in each column et cetera.
43
44     There is currently no weighted version of QuantileNormalizer
45
46     \since New in yat 0.5
47   */
48  class QuantileNormalizer
49  {
50  public:
51    /**
52       \brief perform the quantile normalization.
53
54       It is possible to normalize "in place"; it is permissible for
55       \a matrix and \a result to reference to the same Matrix.
56
57       \note dimensions of \a matrix and \a result must match.
58     */
59    void operator()(const utility::Matrix& matrix,
60                    utility::Matrix& result) const;
61  };
62
63}}} // end of namespace normalizer, yat and thep
64#endif
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