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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 
38 #include <vector>
39 
44 
45 
46 namespace OpenMS
47 {
48 
57  class OPENMS_DLLAPI ItraqQuantifier :
58  public DefaultParamHandler,
59  public ItraqConstants
60  {
61 
62 public:
63 
67 
70 
72  explicit ItraqQuantifier(Int itraq_type);
73 
75  ItraqQuantifier(Int itraq_type, const Param & param);
76 
78  ItraqQuantifier(const ItraqQuantifier & cp);
79 
81  ItraqQuantifier & operator=(const ItraqQuantifier & rhs);
82 
92  void run(const ConsensusMap & consensus_map_in,
93  ConsensusMap & consensus_map_out
94  );
95 
100  {
102  channel_count(0),
103  iso_number_ms2_negative(0),
104  iso_number_reporter_negative(0),
105  iso_number_reporter_different(0),
106  iso_solution_different_intensity(0),
107  iso_total_intensity_negative(0),
108  number_ms2_total(0),
109  number_ms2_empty(0),
110  empty_channels()
111  {
112  }
113 
114  Size channel_count; //< 4plex, 6plex, or 8 plex?!
115  Size iso_number_ms2_negative; //< number of MS2 spectra where one or more channels had negative solution
116  Size iso_number_reporter_negative; //< number of channels where naive solution was negative
117  Size iso_number_reporter_different; //< number of channels >0 where naive solution was different; happens when naive solution is negative in other channels
118  DoubleReal iso_solution_different_intensity; //< absolute intensity difference between both solutions (for channels > 0)
119  DoubleReal iso_total_intensity_negative; //< only for spectra where naive solution is negative
120  Size number_ms2_total; //< total number of MS2 spectra
121  Size number_ms2_empty; //< number of empty MS2 (no reporters at all)
122  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
123  };
124 
125  ItraqQuantifierStats getStats() const;
126 
127 protected:
128 
129  void setDefaultParams_();
130 
131  void updateMembers_();
132 
133 private:
134 
136  void initIsotopeCorrections_();
137 
138  void reconstructChannelInfo_(const ConsensusMap & consensus_map);
139 
145  bool isIdentityCorrectionMatrix_(const Matrix<double>& channel_frequency) const;
146 
149 
153 
156 
159 
160  }; // !class
161 
162  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ItraqQuantifier::ItraqQuantifierStats & stats);
163 
164 } // !namespace
165 
166 #endif // OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
DoubleReal iso_total_intensity_negative
Definition: ItraqQuantifier.h:119
Size channel_count
Definition: ItraqQuantifier.h:114
Int itraq_type_
either ItraqConstants::FOURPLEX or ItraqConstants::EIGHTPLEX
Definition: ItraqQuantifier.h:148
Size number_ms2_total
Definition: ItraqQuantifier.h:120
ItraqConstants::ChannelMapType ChannelMapType
Definition: ItraqQuantifier.h:65
std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)
A container for consensus elements.
Definition: ConsensusMap.h:60
Statistics for quantitation performance and comparison of NNLS vs. naive method (aka matrix inversion...
Definition: ItraqQuantifier.h:99
Some constants used throughout iTRAQ classes.
Definition: ItraqConstants.h:53
Size iso_number_reporter_different
Definition: ItraqQuantifier.h:117
stores information on an iTRAQ channel
Definition: ItraqConstants.h:62
ChannelMapType channel_map_
Definition: ItraqQuantifier.h:152
Size number_ms2_empty
Definition: ItraqQuantifier.h:121
ItraqConstants::IsotopeMatrices IsotopeMatrices
Definition: ItraqQuantifier.h:66
IsotopeMatrices isotope_corrections_
Matrices with isotope correction values (one for each plex-type)
Definition: ItraqQuantifier.h:155
DoubleReal iso_solution_different_intensity
Definition: ItraqQuantifier.h:118
ItraqQuantifierStats stats_
stats for isotope correction
Definition: ItraqQuantifier.h:158
Size iso_number_reporter_negative
Definition: ItraqQuantifier.h:116
Does post-processing on raw iTRAQ channel quantitation.
Definition: ItraqQuantifier.h:57
ItraqQuantifierStats()
Definition: ItraqQuantifier.h:101
Management and storage of parameters / INI files.
Definition: Param.h:69
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Size iso_number_ms2_negative
Definition: ItraqQuantifier.h:115
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:90
ItraqConstants::ChannelInfo ChannelInfo
Definition: ItraqQuantifier.h:64
int Int
Signed integer type.
Definition: Types.h:100
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
std::map< Size, Size > empty_channels
Definition: ItraqQuantifier.h:122

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5