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... | |
| IsobaricIsotopeCorrector & | operator= (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 IsobaricQuantitationMethod * | quant_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... | |
Performs isotope impurity correction on the intensities extracted from an isobaric labeling experiment.
| IsobaricIsotopeCorrector | ( | const IsobaricQuantitationMethod *const | quant_method | ) |
Constructor given an IsobaricQuantitationMethod (e.g., iTRAQ 4 plex).
| quant_method | The quantification method used for the data set to analyze. |
| IsobaricIsotopeCorrector | ( | const IsobaricIsotopeCorrector & | other | ) |
Copy c'tor.
|
virtual |
|
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.
| consensus_map_in | The map containing the values that should be corrected. |
| consensus_map_out | The map where the corrected values should be stored. |
| Exception::FailedAPICall | If the least-squares fit fails. |
| Exception::InvalidParameter | If the given correction matrix is invalid. |
|
private |
Fills the input vector for the gsl/NNLS step given the ConsensusFeature.
|
private |
Free all memory allocated by GSL objects.
Checks if the given matrix is an identity matrix.
| channel_frequency | The matrix to check. |
|
private |
Checks if the gsl matrix is invertible (see IsobaricIsotopeCorrector::gsl_m_).
| IsobaricIsotopeCorrector& operator= | ( | const IsobaricIsotopeCorrector & | rhs | ) |
Assignment operator.
|
private |
Solves the.
|
private |
|
private |
|
private |
Indicates wether memory was allocated for the gsl vector/matrix pointers.
|
private |
|
private |
GSL objects used for the isotope correction.
|
private |
|
private |
|
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 |