MRMRTNormalizer.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
 
#include <cstddef> // for size_t & ptrdiff_t
#include <vector>
#include <string>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MRMRTNormalizer
  {
 
protected:
  
    static int jackknifeOutlierCandidate_(const std::vector<double>& x, const std::vector<double>& y);
 
    static int residualOutlierCandidate_(const std::vector<double>& x, const std::vector<double>& y);
 
public:
 
    static std::vector<std::pair<double, double> > removeOutliersRANSAC(const std::vector<std::pair<double, double> >& pairs,
                                                                        double rsq_limit,
                                                                        double coverage_limit,
                                                                        size_t max_iterations,
                                                                        double max_rt_threshold,
                                                                        size_t sampling_size);
 
    static std::vector<std::pair<double, double> > removeOutliersIterative(const std::vector<std::pair<double, double> >& pairs,
                                                                           double rsq_limit, 
                                                                           double coverage_limit, 
                                                                           bool use_chauvenet,
                                                                           const std::string& method);
 
    static double chauvenet_probability(const std::vector<double>& residuals, int pos);
 
    static bool chauvenet(const std::vector<double>& residuals, int pos);
 
    static bool computeBinnedCoverage(const std::pair<double,double> & rtRange, 
                                      const std::vector<std::pair<double, double> > & pairs,
                                      int nrBins, 
                                      int minPeptidesPerBin,
                                      int minBinsFilled);
 
  };
 
}