OpenMS
2.4.0
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A class that calls the scoring routines. More...
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
Public Member Functions | |
OpenSwathScoring () | |
Constructor. More... | |
~OpenSwathScoring () | |
Destructor. More... | |
void | initialize (double rt_normalization_factor, int add_up_spectra, double spacing_for_spectra_resampling, const OpenSwath_Scores_Usage &su) |
Initialize the scoring object. More... | |
void | calculateChromatographicScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids, const std::string &precursor_chrom_id, const std::vector< double > &normalized_library_intensity, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Scores &scores) |
Score a single peakgroup in a chromatogram using only chromatographic properties. More... | |
void | calculateChromatographicIdScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids_identification, const std::vector< std::string > &native_ids_detection, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Scores &scores) |
Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties. More... | |
void | calculateLibraryScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const CompoundType &compound, const double normalized_feature_rt, OpenSwath_Scores &scores) |
Score a single chromatographic feature against a spectral library. More... | |
void | calculateDIAScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, std::vector< OpenSwath::SwathMap > swath_maps, OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring &diascoring, const CompoundType &compound, OpenSwath_Scores &scores) |
Score a single chromatographic feature using DIA / SWATH scores. More... | |
void | calculatePrecursorDIAScores (OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring &diascoring, double precursor_mz, double rt, const CompoundType &compound, OpenSwath_Scores &scores) |
Score a single chromatographic feature using the precursor map. More... | |
void | calculateDIAIdScores (OpenSwath::IMRMFeature *imrmfeature, const TransitionType &transition, const std::vector< OpenSwath::SwathMap > swath_maps, OpenMS::DIAScoring &diascoring, OpenSwath_Scores &scores) |
Score a single chromatographic feature using DIA / SWATH scores. More... | |
void | getNormalized_library_intensities_ (const std::vector< TransitionType > &transitions, std::vector< double > &normalized_library_intensity) |
Computing the normalized library intensities from the transition objects. More... | |
OpenSwath::SpectrumPtr | getAddedSpectra_ (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add) |
Returns an averaged spectrum. More... | |
OpenSwath::SpectrumPtr | getAddedSpectra_ (std::vector< OpenSwath::SwathMap > swath_maps, double RT, int nr_spectra_to_add) |
Returns an averaged spectrum. More... | |
Private Types | |
typedef OpenSwath::LightCompound | CompoundType |
typedef OpenSwath::LightTransition | TransitionType |
Private Attributes | |
double | rt_normalization_factor_ |
int | add_up_spectra_ |
double | spacing_for_spectra_resampling_ |
OpenSwath_Scores_Usage | su_ |
A class that calls the scoring routines.
Use this class to invoke the individual OpenSWATH scoring routines.
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OpenSwathScoring | ( | ) |
Constructor.
~OpenSwathScoring | ( | ) |
Destructor.
void calculateChromatographicIdScores | ( | OpenSwath::IMRMFeature * | imrmfeature, |
const std::vector< std::string > & | native_ids_identification, | ||
const std::vector< std::string > & | native_ids_detection, | ||
std::vector< OpenSwath::ISignalToNoisePtr > & | signal_noise_estimators, | ||
OpenSwath_Scores & | scores | ||
) |
Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties.
This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. The scores are computed by scoring identification against detection transitions.
The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.
imrmfeature | The feature to be scored |
native_ids_identification | The list of identification native ids (giving a canonical ordering of the transitions) |
native_ids_detection | The list of detection native ids (giving a canonical ordering of the transitions) |
signal_noise_estimators | The signal-to-noise estimators for each transition |
scores | The object to store the result |
void calculateChromatographicScores | ( | OpenSwath::IMRMFeature * | imrmfeature, |
const std::vector< std::string > & | native_ids, | ||
const std::string & | precursor_chrom_id, | ||
const std::vector< double > & | normalized_library_intensity, | ||
std::vector< OpenSwath::ISignalToNoisePtr > & | signal_noise_estimators, | ||
OpenSwath_Scores & | scores | ||
) |
Score a single peakgroup in a chromatogram using only chromatographic properties.
This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. If more information is available, also consider using the library based scoring and the full-spectrum based scoring.
The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.
imrmfeature | The feature to be scored |
native_ids | The list of native ids (giving a canonical ordering of the transitions) |
normalized_library_intensity | The weights to be used for each transition (e.g. normalized library intensities) |
signal_noise_estimators | The signal-to-noise estimators for each transition |
scores | The object to store the result |
void calculateDIAIdScores | ( | OpenSwath::IMRMFeature * | imrmfeature, |
const TransitionType & | transition, | ||
const std::vector< OpenSwath::SwathMap > | swath_maps, | ||
OpenMS::DIAScoring & | diascoring, | ||
OpenSwath_Scores & | scores | ||
) |
Score a single chromatographic feature using DIA / SWATH scores.
The scores are returned in the OpenSwath_Scores object.
imrmfeature | The feature to be scored |
transitions | The library transition to score the feature against |
swath_maps | The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices |
diascoring | DIA Scoring object to use for scoring |
scores | The object to store the result |
void calculateDIAScores | ( | OpenSwath::IMRMFeature * | imrmfeature, |
const std::vector< TransitionType > & | transitions, | ||
std::vector< OpenSwath::SwathMap > | swath_maps, | ||
OpenSwath::SpectrumAccessPtr | ms1_map, | ||
OpenMS::DIAScoring & | diascoring, | ||
const CompoundType & | compound, | ||
OpenSwath_Scores & | scores | ||
) |
Score a single chromatographic feature using DIA / SWATH scores.
The scores are returned in the OpenSwath_Scores object.
imrmfeature | The feature to be scored |
transitions | The library transition to score the feature against |
swath_maps | The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices |
ms1_map | The corresponding MS1 (precursor ion map) from which the precursor spectra can be retrieved (optional, may be NULL) |
diascoring | DIA Scoring object to use for scoring |
pep | The peptide corresponding to the library transitions |
scores | The object to store the result |
void calculateLibraryScores | ( | OpenSwath::IMRMFeature * | imrmfeature, |
const std::vector< TransitionType > & | transitions, | ||
const CompoundType & | compound, | ||
const double | normalized_feature_rt, | ||
OpenSwath_Scores & | scores | ||
) |
Score a single chromatographic feature against a spectral library.
The spectral library is provided in a set of transition objects and a peptide object. Both contain information about the expected elution time on the chromatography and the relative intensity of the transitions.
The scores are returned in the OpenSwath_Scores object.
imrmfeature | The feature to be scored |
transitions | The library transition to score the feature against |
pep | The peptide corresponding to the library transitions |
normalized_feature_rt | The retention time of the feature in normalized space |
scores | The object to store the result |
void calculatePrecursorDIAScores | ( | OpenSwath::SpectrumAccessPtr | ms1_map, |
OpenMS::DIAScoring & | diascoring, | ||
double | precursor_mz, | ||
double | rt, | ||
const CompoundType & | compound, | ||
OpenSwath_Scores & | scores | ||
) |
Score a single chromatographic feature using the precursor map.
The scores are returned in the OpenSwath_Scores object.
ms1_map | The MS1 (precursor ion map) from which the precursor spectra can be retrieved |
diascoring | DIA Scoring object to use for scoring |
precursor_mz | The m/z ratio of the precursor |
rt | The compound retention time |
scores | The object to store the result |
OpenSwath::SpectrumPtr getAddedSpectra_ | ( | OpenSwath::SpectrumAccessPtr | swath_map, |
double | RT, | ||
int | nr_spectra_to_add | ||
) |
Returns an averaged spectrum.
This function will sum up (add) the intensities of multiple spectra around the given retention time and return an "averaged" spectrum which may contain less noise.
[in] | swath_map | The map containing the spectra |
[in] | RT | The target retention time |
[in] | nr_spectra_to_add | How many spectra to add up |
OpenSwath::SpectrumPtr getAddedSpectra_ | ( | std::vector< OpenSwath::SwathMap > | swath_maps, |
double | RT, | ||
int | nr_spectra_to_add | ||
) |
Returns an averaged spectrum.
This function will sum up (add) the intensities of multiple spectra from multiple swath maps (assuming these are SONAR maps of shifted precursor isolation windows) around the given retention time and return an "averaged" spectrum which may contain less noise.
[in] | swath_maps | The maps containing the spectra |
[in] | RT | The target retention time |
[in] | nr_spectra_to_add | How many spectra to add up |
void getNormalized_library_intensities_ | ( | const std::vector< TransitionType > & | transitions, |
std::vector< double > & | normalized_library_intensity | ||
) |
Computing the normalized library intensities from the transition objects.
The intensities are normalized such that the sum to one.
[in] | transitions | The library transition to score the feature against |
[out] | normalized_library_intensity | The resulting normalized library intensities |
void initialize | ( | double | rt_normalization_factor, |
int | add_up_spectra, | ||
double | spacing_for_spectra_resampling, | ||
const OpenSwath_Scores_Usage & | su | ||
) |
Initialize the scoring object.
Sets the parameters for the scoring.
rt_normalization_factor | Specifies the range of the normalized retention time space |
add_up_spectra | How many spectra to add up (default 1) |
spacing_for_spectra_resampling | Spacing factor for spectra addition |
su | Which scores to actually compute |
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