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ItraqQuantifier.h
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34 
35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
36 #define OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
37 
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  class ConsensusMap;
46 
55  class OPENMS_DLLAPI ItraqQuantifier :
56  public DefaultParamHandler,
57  public ItraqConstants
58  {
59 
60 public:
61 
65 
68 
70  explicit ItraqQuantifier(Int itraq_type);
71 
73  ItraqQuantifier(Int itraq_type, const Param& param);
74 
77 
79  ItraqQuantifier& operator=(const ItraqQuantifier& rhs);
80 
90  void run(const ConsensusMap& consensus_map_in, ConsensusMap& consensus_map_out);
91 
96  {
98  channel_count(0),
99  iso_number_ms2_negative(0),
100  iso_number_reporter_negative(0),
101  iso_number_reporter_different(0),
102  iso_solution_different_intensity(0),
103  iso_total_intensity_negative(0),
104  number_ms2_total(0),
105  number_ms2_empty(0),
106  empty_channels()
107  {
108  }
109 
110  Size channel_count; //< 4plex, 6plex, or 8 plex?!
111  Size iso_number_ms2_negative; //< number of MS2 spectra where one or more channels had negative solution
112  Size iso_number_reporter_negative; //< number of channels where naive solution was negative
113  Size iso_number_reporter_different; //< number of channels >0 where naive solution was different; happens when naive solution is negative in other channels
114  double iso_solution_different_intensity; //< absolute intensity difference between both solutions (for channels > 0)
115  double iso_total_intensity_negative; //< only for spectra where naive solution is negative
116  Size number_ms2_total; //< total number of MS2 spectra
117  Size number_ms2_empty; //< number of empty MS2 (no reporters at all)
118  std::map<Size, Size> empty_channels; //< Channel_ID -> Missing; indicating the number of empty channels from all MS2 scans, i.e., numbers are between number_ms2_empty and number_ms2_total
119  };
120 
121  ItraqQuantifierStats getStats() const;
122 
123 protected:
124 
125  void setDefaultParams_();
126 
127  void updateMembers_();
128 
129 private:
130 
132  void initIsotopeCorrections_();
133 
134  void reconstructChannelInfo_(const ConsensusMap& consensus_map);
135 
141  bool isIdentityCorrectionMatrix_(const Matrix<double>& channel_frequency) const;
142 
145 
149 
152 
155 
156  }; // !class
157 
158  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ItraqQuantifier::ItraqQuantifierStats& stats);
159 
160 } // !namespace
161 
162 #endif // OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
Size channel_count
Definition: ItraqQuantifier.h:110
Int itraq_type_
either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ItraqQuantifier.h:144
double iso_total_intensity_negative
Definition: ItraqQuantifier.h:115
Size number_ms2_total
Definition: ItraqQuantifier.h:116
ItraqConstants::ChannelMapType ChannelMapType
Definition: ItraqQuantifier.h:63
A container for consensus elements.
Definition: ConsensusMap.h:72
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: ItraqQuantifier.h:95
double iso_solution_different_intensity
Definition: ItraqQuantifier.h:114
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:53
Size iso_number_reporter_different
Definition: ItraqQuantifier.h:113
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
ChannelMapType channel_map_
Definition: ItraqQuantifier.h:148
Size number_ms2_empty
Definition: ItraqQuantifier.h:117
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ItraqQuantifier.h:64
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ItraqQuantifier.h:151
ItraqQuantifierStats stats_
stats for isotope correction
Definition: ItraqQuantifier.h:154
Size iso_number_reporter_negative
Definition: ItraqQuantifier.h:112
Does post-processing on raw iTRAQ channel quantitation.
Definition: ItraqQuantifier.h:55
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
ItraqQuantifierStats()
Definition: ItraqQuantifier.h:97
Management and storage of parameters / INI files.
Definition: Param.h:75
Size iso_number_ms2_negative
Definition: ItraqQuantifier.h:111
std::vector< Matrix< double > > IsotopeMatrices
(user defined?) isotope correction matrix in (-2, -1, +1, +2) row style
Definition: ItraqConstants.h:75
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
ItraqConstants::ChannelInfo ChannelInfo
Definition: ItraqQuantifier.h:62
int Int
Signed integer type.
Definition: Types.h:96
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
std::map< Size, Size > empty_channels
Definition: ItraqQuantifier.h:118

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:39 using doxygen 1.8.5