OpenMS
IsobaricIsotopeCorrector Class Reference

Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment. More...

#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricIsotopeCorrector.h>

Static Public Member Functions

static IsobaricQuantifierStatistics correctIsotopicImpurities (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, const IsobaricQuantitationMethod *quant_method)
 Apply isotope correction to the given input map and store the corrected values in the output map. More...
 

Static Private Member Functions

static void fillInputVector_ (Eigen::VectorXd &b, Matrix< double > &m_b, const ConsensusFeature &cf, const ConsensusMap &cm)
 Fills the input vector for the Eigen/NNLS step given the ConsensusFeature. More...
 
static void solveNNLS_ (const Matrix< double > &correction_matrix, const Matrix< double > &m_b, Matrix< double > &m_x)
 
static void computeStats_ (const Matrix< double > &m_x, const Eigen::MatrixXd &x, const float cf_intensity, const IsobaricQuantitationMethod *quant_method, IsobaricQuantifierStatistics &stats)
 
static float updateOutpuMap_ (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, Size current_cf, const Matrix< double > &m_x)
 

Detailed Description

Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment.

Member Function Documentation

◆ computeStats_()

static void computeStats_ ( const Matrix< double > &  m_x,
const Eigen::MatrixXd x,
const float  cf_intensity,
const IsobaricQuantitationMethod quant_method,
IsobaricQuantifierStatistics stats 
)
staticprivate

◆ correctIsotopicImpurities()

static IsobaricQuantifierStatistics correctIsotopicImpurities ( const ConsensusMap consensus_map_in,
ConsensusMap consensus_map_out,
const IsobaricQuantitationMethod quant_method 
)
static

Apply isotope correction to the given input map and store the corrected values in the output map.

Parameters
consensus_map_inThe map containing the values that should be corrected.
consensus_map_outThe map where the corrected values should be stored.
IsobaricQuantitationMethod(e.g., iTRAQ 4 plex)
Exceptions
Exception::FailedAPICallIf the least-squares fit fails.
Exception::InvalidParameterIf the given correction matrix is invalid.

◆ fillInputVector_()

static void fillInputVector_ ( Eigen::VectorXd b,
Matrix< double > &  m_b,
const ConsensusFeature cf,
const ConsensusMap cm 
)
staticprivate

Fills the input vector for the Eigen/NNLS step given the ConsensusFeature.

◆ solveNNLS_()

static void solveNNLS_ ( const Matrix< double > &  correction_matrix,
const Matrix< double > &  m_b,
Matrix< double > &  m_x 
)
staticprivate

◆ updateOutpuMap_()

static float updateOutpuMap_ ( const ConsensusMap consensus_map_in,
ConsensusMap consensus_map_out,
Size  current_cf,
const Matrix< double > &  m_x 
)
staticprivate