1 | // $Id: QuantileNormalizer.cc 1497 2008-09-12 18:30:41Z 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 3 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 yat. If not, see <http://www.gnu.org/licenses/>. |
---|
22 | */ |
---|
23 | |
---|
24 | #include "QuantileNormalizer.h" |
---|
25 | |
---|
26 | #include "yat/statistics/Averager.h" |
---|
27 | |
---|
28 | #include "yat/utility/Matrix.h" |
---|
29 | #include "yat/utility/VectorConstView.h" |
---|
30 | |
---|
31 | #include <cassert> |
---|
32 | |
---|
33 | namespace theplu { |
---|
34 | namespace yat { |
---|
35 | namespace normalizer { |
---|
36 | |
---|
37 | void QuantileNormalizer::operator()(const utility::Matrix& data, |
---|
38 | utility::Matrix& result) const |
---|
39 | { |
---|
40 | assert(data.rows()==result.rows()); |
---|
41 | utility::Matrix data_copy(data); |
---|
42 | |
---|
43 | // sort columns in copy |
---|
44 | for (size_t column=0; column<data_copy.columns(); ++column){ |
---|
45 | std::sort(data_copy.begin_column(column), data_copy.end_column(column)); |
---|
46 | } |
---|
47 | |
---|
48 | // calculate average of each row |
---|
49 | std::vector<yat::statistics::Averager> averager(data_copy.rows()); |
---|
50 | for (size_t row=0; row<data_copy.rows(); ++row){ |
---|
51 | add(averager[row], data_copy.begin_row(row), data_copy.end_row(row)); |
---|
52 | } |
---|
53 | |
---|
54 | for (size_t column=0; column<result.columns(); ++column){ |
---|
55 | std::vector<size_t> index; |
---|
56 | utility::sort_index(index, result.column_const_view(column)); |
---|
57 | |
---|
58 | for (size_t row=0; row<result.rows(); ++row) |
---|
59 | result(index[row], column) = averager[row].mean(); |
---|
60 | } |
---|
61 | } |
---|
62 | |
---|
63 | |
---|
64 | |
---|
65 | }}} // end of namespace utility, yat and thep |
---|