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IsobaricIsotopeCorrector Class Reference

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

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

Public Member Functions

 IsobaricIsotopeCorrector (const IsobaricQuantitationMethod *const quant_method)
 Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex). More...
 
 IsobaricIsotopeCorrector (const IsobaricIsotopeCorrector &other)
 Copy c'tor. More...
 
IsobaricIsotopeCorrectoroperator= (const IsobaricIsotopeCorrector &rhs)
 Assignment operator. More...
 
virtual ~IsobaricIsotopeCorrector ()
 
IsobaricQuantifierStatistics correctIsotopicImpurities (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out)
 Apply isotope correction to the given input map and store the corrected values in the output map. More...
 

Private Member Functions

bool isIdentityMatrix_ (const Matrix< double > &channel_frequency) const
 Checks if the given matrix is an identity matrix. More...
 
bool isInvertible_ () const
 Checks if the gsl matrix is invertible (see IsobaricIsotopeCorrector::gsl_m_). More...
 
void fillInputVector_ (gsl_vector *gsl_b, Matrix< double > &m_b, const ConsensusFeature &cf, const ConsensusMap &cm) const
 Fills the input vector for the gsl/NNLS step given the ConsensusFeature. More...
 
void solveGSL_ (const gsl_matrix *gsl_m, const gsl_permutation *gsl_p, const gsl_vector *gsl_b, gsl_vector *gsl_x) const
 Solves the. More...
 
void solveNNLS_ (const Matrix< double > &correction_matrix, const Matrix< double > &m_b, Matrix< double > &m_x) const
 
void computeStats_ (const Matrix< double > &m_x, gsl_vector *gsl_x, const ConsensusFeature::IntensityType cf_intensity, IsobaricQuantifierStatistics &stats)
 
ConsensusFeature::IntensityType updateOutpuMap_ (const ConsensusMap &consensus_map_in, ConsensusMap &consensus_map_out, ConsensusMap::size_type current_cf, const Matrix< double > &m_x) const
 

Private Attributes

const IsobaricQuantitationMethodquant_method_
 The quantification method used for the dataset to be analyzed. More...
 
gsl_matrix * gsl_m_
 GSL objects used for the isotope correction. More...
 
gsl_permutation * gsl_p_
 
gsl_vector * gsl_b_
 
gsl_vector * gsl_x_
 
bool gsl_allocated_
 Indicates wether memory was allocated for the gsl vector/matrix pointers. More...
 
void freeGSLMemory_ ()
 Free all memory allocated by GSL objects. More...
 

Detailed Description

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

Constructor & Destructor Documentation

IsobaricIsotopeCorrector ( const IsobaricQuantitationMethod *const  quant_method)

Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).

Parameters
quant_methodThe quantification method used for the data set to analyze.

Copy c'tor.

virtual ~IsobaricIsotopeCorrector ( )
virtual

Member Function Documentation

void computeStats_ ( const Matrix< double > &  m_x,
gsl_vector *  gsl_x,
const ConsensusFeature::IntensityType  cf_intensity,
IsobaricQuantifierStatistics stats 
)
private
IsobaricQuantifierStatistics correctIsotopicImpurities ( const ConsensusMap consensus_map_in,
ConsensusMap consensus_map_out 
)

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.
Exceptions
Exception::FailedAPICallIf the least-squares fit fails.
Exception::InvalidParameterIf the given correction matrix is invalid.
void fillInputVector_ ( gsl_vector *  gsl_b,
Matrix< double > &  m_b,
const ConsensusFeature cf,
const ConsensusMap cm 
) const
private

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

void freeGSLMemory_ ( )
private

Free all memory allocated by GSL objects.

bool isIdentityMatrix_ ( const Matrix< double > &  channel_frequency) const
private

Checks if the given matrix is an identity matrix.

Parameters
channel_frequencyThe matrix to check.
Returns
True if the given matrix is an identity matrix, false otherwise.
bool isInvertible_ ( ) const
private

Checks if the gsl matrix is invertible (see IsobaricIsotopeCorrector::gsl_m_).

Returns
True if the matrix is invertible, false otherwise.

Assignment operator.

void solveGSL_ ( const gsl_matrix *  gsl_m,
const gsl_permutation *  gsl_p,
const gsl_vector *  gsl_b,
gsl_vector *  gsl_x 
) const
private

Solves the.

void solveNNLS_ ( const Matrix< double > &  correction_matrix,
const Matrix< double > &  m_b,
Matrix< double > &  m_x 
) const
private
ConsensusFeature::IntensityType updateOutpuMap_ ( const ConsensusMap consensus_map_in,
ConsensusMap consensus_map_out,
ConsensusMap::size_type  current_cf,
const Matrix< double > &  m_x 
) const
private

Member Data Documentation

bool gsl_allocated_
private

Indicates wether memory was allocated for the gsl vector/matrix pointers.

gsl_vector* gsl_b_
private
gsl_matrix* gsl_m_
private

GSL objects used for the isotope correction.

gsl_permutation* gsl_p_
private
gsl_vector* gsl_x_
private
const IsobaricQuantitationMethod* quant_method_
private

The quantification method used for the dataset to be analyzed.


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5