| OpenMS 2.5.0

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>`

## 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.