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... | |
| Int | 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... | |
Performs median normalization on the extracted ratios of isobaric labeling experiment.
| IsobaricNormalizer | ( | const IsobaricQuantitationMethod *const | quant_method | ) | 
Default c'tor.
| IsobaricNormalizer | ( | const IsobaricNormalizer & | other | ) | 
Copy c'tor.
| 
 | private | 
Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors.
| consensus_map | The consensus map for which the mapping should be build. | 
| 
 | private | 
Collects ratios and intensities for a given ConsensusFeature.
| cf | The consensus feature to evaluate. | 
| ref_intensity | The intensity of the reference channel. | 
| 
 | private | 
Computes the normalization factors from the given peptide ratios.
| normalization_factors | The normalization factors to compute. | 
| 
 | private | 
Given a ConsensusFeature the method will return an iterator pointing to the consensus element representing the reference channel.
| cf | The ConsensusFeature for which the reference element should be found. | 
| consensus_map | The ConsensusMap in which the reference element should be found. | 
| void normalize | ( | ConsensusMap & | consensus_map | ) | 
Normalizes the intensity ratios in the given input map (using median).
| consensus_map | The map to normalize. | 
| IsobaricNormalizer& operator= | ( | const IsobaricNormalizer & | rhs | ) | 
Assignment operator.
The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors.
| 
 | private | 
Collection containing the collected peptide intensities for the individual channels.
| 
 | private | 
Collection containing the collected peptide ratios for the individual channels.
| 
 | private | 
The selected quantitation method that will be used for the normalization.
| 
 | private | 
The index of the reference channel in the peptide ratio/intensity vectors.
| 
 | private | 
The name of the reference channel as given in the IsobaricChannelInformation.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |