source: trunk/yat/normalization/QuantileNormalizer.cc @ 1447

Last change on this file since 1447 was 1447, checked in by Peter, 13 years ago

Changed the interface of QuantileNormalizer?. The interface now has one matrix& and one const&. The former is object for normalization, and the latter is the base for calculating the distributions (Quantiles). The reason to change the interface is to allow normalization based on a nother matrix, e.g., normalizing a test data matrix based on the training data matrix. Also it is more inline with the Centralizer added earlier today. refs #425

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 2.0 KB
RevLine 
[327]1// $Id: QuantileNormalizer.cc 1447 2008-08-28 02:56:42Z peter $
2
[570]3/*
[831]4  Copyright (C) 2005, 2006 Jari Häkkinen, Markus Ringnér
[1275]5  Copyright (C) 2007 Jari Häkkinen, Peter Johansson
[1432]6  Copyright (C) 2008 Peter Johansson
[570]7
[1432]8  This file is part of the yat library, http://dev.thep.lu.se/yat
[570]9
[675]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.
[570]14
[675]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
[570]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
[1432]26#include "QuantileNormalizer.h"
[734]27
[1304]28#include "yat/statistics/Averager.h"
[435]29
[1432]30#include "yat/utility/Matrix.h"
31#include "yat/utility/VectorConstView.h"
[327]32
33namespace theplu {
[680]34namespace yat {
[1432]35namespace normalization {
[327]36
[1447]37  void QuantileNormalizer::operator()(const utility::Matrix& data,
38                                      utility::Matrix& result) const
[435]39  {
[1432]40    utility::Matrix data_copy(data);
[1304]41   
42    // sort columns in copy
43    for (size_t column=0; column<data_copy.columns(); ++column){
44      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
45    }
[616]46
[1304]47    // calculate average of each row
48    std::vector<yat::statistics::Averager> averager(data_copy.rows());
49    for (size_t row=0; row<data_copy.rows(); ++row){
50      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
51    }
52
[1447]53    for (size_t column=0; column<result.columns(); ++column){
[1304]54      std::vector<size_t> index;
[1447]55      utility::sort_index(index, result.column_const_view(column));
[1304]56                               
[1447]57      for (size_t row=0; row<result.rows(); ++row)
58        result(index[row], column) = averager[row].mean();
[1304]59    }
60  }
61
62
63
[680]64}}} // end of namespace utility, yat and thep
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