1 | // $Id: QuantileNormalizer.cc 1486 2008-09-09 21:17:19Z jari $ |
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2 | |
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3 | /* |
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4 | Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér |
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5 | Copyright (C) 2007 Jari Häkkinen, Peter Johansson |
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6 | Copyright (C) 2008 Peter Johansson |
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7 | |
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8 | This file is part of the yat library, http://dev.thep.lu.se/yat |
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9 | |
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10 | The yat library is free software; you can redistribute it and/or |
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11 | modify it under the terms of the GNU General Public License as |
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12 | published by the Free Software Foundation; either version 3 of the |
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13 | License, or (at your option) any later version. |
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14 | |
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15 | The yat library is distributed in the hope that it will be useful, |
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16 | but WITHOUT ANY WARRANTY; without even the implied warranty of |
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17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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18 | General Public License for more details. |
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19 | |
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20 | You should have received a copy of the GNU General Public License |
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21 | along with this program; if not, write to the Free Software |
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22 | Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA |
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23 | 02111-1307, USA. |
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24 | */ |
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25 | |
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26 | #include "QuantileNormalizer.h" |
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27 | |
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28 | #include "yat/statistics/Averager.h" |
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29 | |
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30 | #include "yat/utility/Matrix.h" |
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31 | #include "yat/utility/VectorConstView.h" |
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32 | |
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33 | #include <cassert> |
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34 | |
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35 | namespace theplu { |
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36 | namespace yat { |
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37 | namespace normalization { |
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38 | |
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39 | void QuantileNormalizer::operator()(const utility::Matrix& data, |
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40 | utility::Matrix& result) const |
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41 | { |
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42 | assert(data.rows()==result.rows()); |
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43 | utility::Matrix data_copy(data); |
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44 | |
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45 | // sort columns in copy |
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46 | for (size_t column=0; column<data_copy.columns(); ++column){ |
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47 | std::sort(data_copy.begin_column(column), data_copy.end_column(column)); |
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48 | } |
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49 | |
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50 | // calculate average of each row |
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51 | std::vector<yat::statistics::Averager> averager(data_copy.rows()); |
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52 | for (size_t row=0; row<data_copy.rows(); ++row){ |
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53 | add(averager[row], data_copy.begin_row(row), data_copy.end_row(row)); |
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54 | } |
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55 | |
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56 | for (size_t column=0; column<result.columns(); ++column){ |
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57 | std::vector<size_t> index; |
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58 | utility::sort_index(index, result.column_const_view(column)); |
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59 | |
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60 | for (size_t row=0; row<result.rows(); ++row) |
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61 | result(index[row], column) = averager[row].mean(); |
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62 | } |
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63 | } |
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64 | |
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65 | |
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66 | |
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67 | }}} // end of namespace utility, yat and thep |
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