OpenMS  2.8.0
Public Member Functions | Private Member Functions | Private Attributes | List of all members
IsobaricNormalizer Class Reference

Performs median normalization on the extracted ratios of isobaric labeling experiment. More...

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

Collaboration diagram for IsobaricNormalizer:
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Public Member Functions

 IsobaricNormalizer (const IsobaricQuantitationMethod *const quant_method)
 Default c'tor. More...
 
 IsobaricNormalizer (const IsobaricNormalizer &other)
 Copy c'tor. More...
 
IsobaricNormalizeroperator= (const IsobaricNormalizer &rhs)
 Assignment operator. More...
 
void normalize (ConsensusMap &consensus_map)
 Normalizes the intensity ratios in the given input map (using median). More...
 

Private Member Functions

ConsensusFeature::HandleSetType::iterator findReferenceChannel_ (ConsensusFeature &cf, const ConsensusMap &consensus_map) const
 Given a ConsensusFeature the method will return an iterator pointing to the consensus element representing the reference channel. More...
 
void buildVectorIndex_ (const ConsensusMap &consensus_map)
 Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors. More...
 
void collectRatios_ (const ConsensusFeature &cf, const Peak2D::IntensityType &ref_intensity)
 Collects ratios and intensities for a given ConsensusFeature. More...
 
void computeNormalizationFactors_ (std::vector< Peak2D::IntensityType > &normalization_factors)
 Computes the normalization factors from the given peptide ratios. More...
 

Private Attributes

const IsobaricQuantitationMethodquant_meth_
 The selected quantitation method that will be used for the normalization. More...
 
String reference_channel_name_
 The name of the reference channel as given in the IsobaricChannelInformation. More...
 
Map< Size, Sizemap_to_vec_index_
 The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors. More...
 
Size ref_map_id_
 The index of the reference channel in the peptide ratio/intensity vectors. More...
 
std::vector< std::vector< Peak2D::IntensityType > > peptide_ratios_
 Collection containing the collected peptide ratios for the individual channels. More...
 
std::vector< std::vector< Peak2D::IntensityType > > peptide_intensities_
 Collection containing the collected peptide intensities for the individual channels. More...
 

Detailed Description

Performs median normalization on the extracted ratios of isobaric labeling experiment.

Constructor & Destructor Documentation

◆ IsobaricNormalizer() [1/2]

IsobaricNormalizer ( const IsobaricQuantitationMethod *const  quant_method)
explicit

Default c'tor.

◆ IsobaricNormalizer() [2/2]

Copy c'tor.

Member Function Documentation

◆ buildVectorIndex_()

void buildVectorIndex_ ( const ConsensusMap consensus_map)
private

Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors.

Parameters
consensus_mapThe consensus map for which the mapping should be build.

◆ collectRatios_()

void collectRatios_ ( const ConsensusFeature cf,
const Peak2D::IntensityType ref_intensity 
)
private

Collects ratios and intensities for a given ConsensusFeature.

Parameters
cfThe consensus feature to evaluate.
ref_intensityThe intensity of the reference channel.

◆ computeNormalizationFactors_()

void computeNormalizationFactors_ ( std::vector< Peak2D::IntensityType > &  normalization_factors)
private

Computes the normalization factors from the given peptide ratios.

Parameters
normalization_factorsThe normalization factors to compute.

◆ findReferenceChannel_()

ConsensusFeature::HandleSetType::iterator findReferenceChannel_ ( ConsensusFeature cf,
const ConsensusMap consensus_map 
) const
private

Given a ConsensusFeature the method will return an iterator pointing to the consensus element representing the reference channel.

Parameters
cfThe ConsensusFeature for which the reference element should be found.
consensus_mapThe ConsensusMap in which the reference element should be found.
Returns
An iterator pointing to the consensus element of the reference channel. ConsensusFeature::end() if the reference channel is not contained.

◆ normalize()

void normalize ( ConsensusMap consensus_map)

Normalizes the intensity ratios in the given input map (using median).

Parameters
consensus_mapThe map to normalize.

◆ operator=()

IsobaricNormalizer& operator= ( const IsobaricNormalizer rhs)

Assignment operator.

Member Data Documentation

◆ map_to_vec_index_

Map<Size, Size> map_to_vec_index_
private

The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors.

◆ peptide_intensities_

std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_
private

Collection containing the collected peptide intensities for the individual channels.

◆ peptide_ratios_

std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_
private

Collection containing the collected peptide ratios for the individual channels.

◆ quant_meth_

const IsobaricQuantitationMethod* quant_meth_
private

The selected quantitation method that will be used for the normalization.

◆ ref_map_id_

Size ref_map_id_
private

The index of the reference channel in the peptide ratio/intensity vectors.

◆ reference_channel_name_

String reference_channel_name_
private

The name of the reference channel as given in the IsobaricChannelInformation.