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OpenMS
2.4.0
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TOPPMetaProSIP () | |
Protected Member Functions | |
void | registerOptionsAndFlags_ () override |
void | filterIsotopicIntensities (vector< double >::const_iterator &pattern_begin, vector< double >::const_iterator &pattern_end, vector< double >::const_iterator &intensities_begin, vector< double >::const_iterator &intensities_end, double TIC_threshold=0.99) |
> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation More... | |
void | calculateCorrelation (Size n_element, const vector< double > &isotopic_intensities, IsotopePatterns patterns, MapRateToScoreType &map_rate_to_correlation_score, String labeling_element, double mass, double min_correlation_distance_to_averagine) |
Returns highest scoring rate and score pair in the map. More... | |
void | getBestRateScorePair (const MapRateToScoreType &map_rate_to_score, double &best_rate, double &best_score) |
PeakSpectrum | extractPeakSpectrum (Size element_count, double mass_diff, double rt, double feature_hit_theoretical_mz, Int feature_hit_charge, const PeakMap &peak_map) |
vector< double > | extractIsotopicIntensities (Size element_count, double mass_diff, double mz_tolerance_ppm, double seed_rt, double seed_mz, double seed_charge, const PeakMap &peak_map) |
void | writePeakIntensities_ (SVOutStream &out_stream, vector< double > isotopic_intensities, bool write_13Cpeaks) |
MapRateToScoreType | normalizeToMax (const MapRateToScoreType &map_rate_to_decomposition_weight) |
vector< double > | findApexRT (const FeatureMap::iterator feature_it, double hit_rt, const PeakMap &peak_map, Size n_scans) |
PeakSpectrum | mergeSpectra (const PeakMap &to_merge) |
PeakSpectrum | isotopicIntensitiesToSpectrum (double mz_start, double mass_diff, Int charge, vector< double > isotopic_intensities) |
> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size More... | |
void | extractIncorporationsAtCorrelationMaxima (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_decomposition_weight=10.0) |
void | extractIncorporationsAtHeighestDecompositionWeights (SIPPeptide &sip_peptide, const IsotopePatterns &patterns, double weight_merge_window=5.0, double min_corr_threshold=0.5, double min_low_RIA_threshold=-1, double min_decomposition_weight=10.0) |
> Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window. More... | |
double | calculateGlobalLR (const vector< double > &isotopic_intensities) |
> calculate the global labeling ration based on all but the first 4 peaks More... | |
ExitCodes | main_ (int, const char **) override |
Protected Attributes | |
Size | ADDITIONAL_ISOTOPES |
std::string | FEATURE_STRING |
std::string | UNASSIGNED_ID_STRING |
std::string | UNIDENTIFIED_STRING |
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Returns highest scoring rate and score pair in the map.
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> calculate the global labeling ration based on all but the first 4 peaks
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> Collect decomposition coefficients in the merge window around the correlation maximum. > Final list of RIAs is constructed for the peptide.
References SIPIncorporation::abundance, SIPPeptide::charge, SIPIncorporation::correlation, SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, SIPPeptide::decomposition_map, SIPPeptide::explained_TIC_fraction, SIPPeptide::incorporations, SIPPeptide::mass_diff, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, and SIPIncorporation::rate.
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> Collect decomposition coefficients. Starting at the largest decomposition weights merge smaller weights in the merge window.
References SIPIncorporation::abundance, SIPPeptide::charge, SIPIncorporation::correlation, SIPPeptide::correlation_map, SIPPeptide::decomposition_map, SIPPeptide::explained_TIC_fraction, SIPPeptide::incorporations, SIPPeptide::mass_diff, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, and SIPIncorporation::rate.
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> filter intensity to remove noise or additional incorporation peaks that otherwise might interfere with correlation calculation
Calculates the correlation between measured isotopic_intensities and the theoretical isotopic patterns for all incorporation rates
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> converts a vector of isotopic intensities to a peak spectrum starting at mz=mz_start with mass_diff/charge step size
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< number of PSMs. If 0 IDMapper has not been called.
References SIPPeptide::accessions, SIPPeptide::accumulated, MetaProSIPDecomposition::calculateDecompositionWeightsIsotopicPatterns(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor13CRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor15NRangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORange(), MetaProSIPDecomposition::calculateIsotopePatternsFor18ORangeOfAveraginePeptide(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRange(), MetaProSIPDecomposition::calculateIsotopePatternsFor2HRangeOfAveraginePeptide(), SIPPeptide::charge, RIntegration::checkRDependencies(), MetaProSIPClustering::clusterSIPPeptides(), SIPPeptide::correlation_map, SIPPeptide::correlation_maxima, MetaProSIPReporting::createCSVReport(), MetaProSIPReporting::createPeptideCentricCSVReport(), MetaProSIPReporting::createQualityReport(), SIPPeptide::decomposition_map, MetaProSIPXICExtraction::extractXICsOfIsotopeTraces(), SIPPeptide::feature_mz, SIPPeptide::feature_rt, SIPPeptide::feature_type, MetaProSIPInterpolation::getHighPoints(), MetaProSIPDecomposition::getNumberOfLabelingElements(), MetaProSIPClustering::getRIAClusterCenter(), SIPPeptide::global_LR, SIPPeptide::incorporations, SIPPeptide::mass_diff, SIPPeptide::mass_theo, SIPPeptide::mz_theo, SIPPeptide::patterns, SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, SIPPeptide::score, SIPPeptide::sequence, and SIPPeptide::unique.
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