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