FalseDiscoveryRate.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 2002-2020.
//
// 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: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
 
#include <boost/unordered_map.hpp>
 
#include <vector>
#include <unordered_set>
 
namespace OpenMS
{
 
  struct ScoreToTgtDecLabelPairs;
 
  class OPENMS_DLLAPI FalseDiscoveryRate :
    public DefaultParamHandler
  {
public:
    FalseDiscoveryRate();
 
    void apply(std::vector<PeptideIdentification>& fwd_ids, std::vector<PeptideIdentification>& rev_ids) const;
 
    void apply(std::vector<PeptideIdentification>& id) const;
 
    void apply(std::vector<ProteinIdentification>& fwd_ids, std::vector<ProteinIdentification>& rev_ids) const;
 
    void apply(std::vector<ProteinIdentification>& ids) const;
 
    void applyEstimated(std::vector<ProteinIdentification>& ids) const;
 
    double applyEvaluateProteinIDs(const std::vector<ProteinIdentification>& ids, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2);
    double applyEvaluateProteinIDs(const ProteinIdentification& ids, double pepCutoff = 1.0, UInt fpCutoff = 50, double diffWeight = 0.2);
 
    void applyBasic(std::vector<PeptideIdentification> & ids);
    void applyBasic(ConsensusMap & cmap, bool use_unassigned_peptides = true);
    void applyBasic(ProteinIdentification & id, bool groups_too = true);
 
    double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff) const;
 
    double rocN(const std::vector<PeptideIdentification>& ids, Size fp_cutoff, const String& identifier) const;
 
    double rocN(const ConsensusMap& ids, Size fp_cutoff) const;
 
    double rocN(const ConsensusMap& ids, Size fp_cutoff, const String& identifier) const;
 
    IdentificationData::ScoreTypeRef applyToQueryMatches(IdentificationData& id_data, IdentificationData::ScoreTypeRef score_ref) const;
 
 
private:
 
    FalseDiscoveryRate(const FalseDiscoveryRate&);
 
    FalseDiscoveryRate& operator=(const FalseDiscoveryRate&);
 
    void calculateFDRs_(std::map<double, double>& score_to_fdr, std::vector<double>& target_scores, std::vector<double>& decoy_scores, bool q_value, bool higher_score_better) const;
 
    void handleQueryMatch_(
        IdentificationData::QueryMatchRef match_ref,
        IdentificationData::ScoreTypeRef score_ref,
        std::vector<double>& target_scores,
        std::vector<double>& decoy_scores,
        std::map<IdentificationData::IdentifiedMoleculeRef, bool>& molecule_to_decoy,
        std::map<IdentificationData::QueryMatchRef, double>& match_to_score) const;
 
    void calculateEstimatedQVal_(std::map<double, double> &scores_to_FDR,
                                 ScoreToTgtDecLabelPairs &scores_labels,
                                 bool higher_score_better) const;
 
    void calculateFDRBasic_(std::map<double,double>& scores_to_FDR, ScoreToTgtDecLabelPairs& scores_labels, bool qvalue, bool higher_score_better) const;
 
    //TODO the next two methods could potentially be merged for speed (they iterate over the same structure)
    //But since they have different cutoff types and it is more generic, I leave it like this.
    double diffEstimatedEmpirical_(const ScoreToTgtDecLabelPairs& scores_labels, double pepCutoff = 1.0) const;
 
    double rocN_(const ScoreToTgtDecLabelPairs& scores_labels, Size fpCutoff = 50) const;
 
    double trapezoidal_area_xEqy(double exp1, double exp2, double act1, double act2) const;
 
    double trapezoidal_area(double x1, double x2, double y1, double y2) const;
 
  };
 
} // namespace OpenMS