35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
36 #define OPENMS_ANALYSIS_QUANTITATION_ITRAQQUANTIFIER_H
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),
129 void setDefaultParams_();
131 void updateMembers_();
136 void initIsotopeCorrections_();
138 void reconstructChannelInfo_(
const ConsensusMap & consensus_map);
145 bool isIdentityCorrectionMatrix_(
const Matrix<double>& channel_frequency)
const;
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