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| OpenSwathWorkflow (bool use_ms1_traces) |
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TransformationDescription | performRTNormalization (const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const String &mz_correction_function, Size debug_level) |
| Compute the alignment against a set of RT-normalization peptides. More...
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void | performExtraction (const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &cp, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, Interfaces::IMSDataConsumer<> *chromConsumer, int batchSize, bool load_into_memory) |
| Execute the OpenSWATH workflow on a set of SwathMaps and transitions. More...
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void | selectPeptidesForBatch_ (const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j) |
| Select which peptides to analyze in the next batch (and copy to output) More...
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void | copyBatchTransitions_ (const std::vector< OpenSwath::LightPeptide > &used_peptides, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output) |
| Copy the required transitions to output. More...
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void | simpleExtractChromatograms (const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram<> > &chromatograms, const ChromExtractParams &cp) |
| Simple method to extract chromatograms (for the RT-normalization peptides) More...
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TransformationDescription | RTNormalization (TargetedExperiment transition_exp_, std::vector< OpenMS::MSChromatogram<> > chromatograms, double min_rsq, double min_coverage, Param feature_finder_param, const Param &irt_detection_param, std::vector< OpenSwath::SwathMap > &swath_maps, const String &mz_correction_function) |
| Perform RT normalization using the MRMFeatureFinderScoring. More...
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bool | computeBinnedCoverage (const std::pair< double, double > &rtRange, const std::vector< std::pair< double, double > > &pairs, int nrBins, int minPeptidesPerBin, int minBinsFilled) |
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void | scoreAllChromatograms (const OpenSwath::SpectrumAccessPtr input, const OpenSwath::SpectrumAccessPtr swath_map, OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms) |
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void | prepare_coordinates_wrap (std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, OpenSwath::LightTargetedExperiment &transition_exp_used, const bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const |
| Wrapper function for prepare_coordinates that also correctly handles transformations. More...
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void | prepare_coordinates (std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1) const |
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void | selectChrom_ (const MSChromatogram< ChromatogramPeak > &chromatogram_old, MSSpectrum< ChromatogramPeak > &chromatogram, double rt_extraction_window, double center_rt) |
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Class to execute an OpenSwath Workflow.
performExtraction will perform the OpenSWATH analysis. Optionally, an RT transformation (mapping peptides to normalized space) can be obtained beforehand using performRTNormalization.
void performExtraction |
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const std::vector< OpenSwath::SwathMap > & |
swath_maps, |
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const TransformationDescription |
trafo, |
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const ChromExtractParams & |
cp, |
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const Param & |
feature_finder_param, |
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const OpenSwath::LightTargetedExperiment & |
transition_exp, |
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FeatureMap & |
out_featureFile, |
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bool |
store_features, |
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OpenSwathTSVWriter & |
tsv_writer, |
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Interfaces::IMSDataConsumer<> * |
chromConsumer, |
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int |
batchSize, |
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bool |
load_into_memory |
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Execute the OpenSWATH workflow on a set of SwathMaps and transitions.
Executes the following operations on the given input:
1. OpenSwathHelper::selectSwathTransitions 2. ChromatogramExtractor prepare, extract 3. scoreAllChromatograms 4. Write out chromatograms and found features
- Parameters
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swath_maps | The raw data (swath maps) |
trafo | Transformation description (translating this runs' RT to normalized RT space) |
cp | Parameter set for the chromatogram extraction |
feature_finder_param | Parameter set for the feature finding in chromatographic dimension |
transition_exp | The set of assays to be extracted and scored |
out_featureFile | Output feature map to store identified features |
store_features | Whether features should be appended to the output feature map |
tsv_writer | TSV Writer object to store identified features in csv format |
chromConsumer | Chromatogram consumer object to store the extracted chromatograms |
batchSize | Size of the batches which should be extracted and scored |
References OpenSwathWorkflow::ChromExtractParams::extraction_function, OpenSwathWorkflow::ChromExtractParams::min_upper_edge_dist, OpenSwathWorkflow::ms1_map_, OpenSwathWorkflow::ChromExtractParams::mz_extraction_window, OpenSwathWorkflow::ChromExtractParams::ppm, OpenSwathWorkflow::prepare_coordinates_wrap(), OpenSwathWorkflow::ChromExtractParams::rt_extraction_window, OpenSwathWorkflow::scoreAllChromatograms(), OpenSwathWorkflow::selectPeptidesForBatch_(), OpenSwathWorkflow::use_ms1_traces_, and OpenSwathTSVWriter::writeHeader().