35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H 36 #define OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H 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),
125 void setDefaultParams_();
127 void updateMembers_();
132 void initIsotopeCorrections_();
134 void reconstructChannelInfo_(
const ConsensusMap& consensus_map);
141 bool isIdentityCorrectionMatrix_(
const Matrix<double>& channel_frequency)
const;
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
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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