IsobaricNormalizer Class Reference

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

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

Public Member Functions
	IsobaricNormalizer (const IsobaricQuantitationMethod *const quant_method)
	Default c'tor. More...
	IsobaricNormalizer (const IsobaricNormalizer &other)
	Copy c'tor. More...
IsobaricNormalizer &	operator= (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 IsobaricQuantitationMethod *	quant_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, Size >	map_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]

IsobaricNormalizer

(

const IsobaricNormalizer &

other

)

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_map

The 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

cf	The consensus feature to evaluate.
ref_intensity	The 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_factors

The 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

cf	The ConsensusFeature for which the reference element should be found.
consensus_map	The 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_map

The 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.