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OpenMS
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Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis). More...
#include <OpenMS/FILTERING/DATAREDUCTION/FeatureFindingMetabo.h>
Public Member Functions | |
| FeatureHypothesis ()=default | |
| default constructor More... | |
| ~FeatureHypothesis ()=default | |
| default destructor More... | |
| FeatureHypothesis (const FeatureHypothesis &)=default | |
| copy constructor More... | |
| FeatureHypothesis & | operator= (const FeatureHypothesis &rhs)=default |
| assignment operator More... | |
| Size | getSize () const |
| String | getLabel () const |
| std::vector< String > | getLabels () const |
| double | getScore () const |
| void | setScore (const double &score) |
| SignedSize | getCharge () const |
| void | setCharge (const SignedSize &ch) |
| std::vector< double > | getAllIntensities (bool smoothed=false) const |
| std::vector< double > | getAllCentroidMZ () const |
| std::vector< double > | getAllCentroidRT () const |
| std::vector< double > | getIsotopeDistances () const |
| double | getCentroidMZ () const |
| double | getCentroidRT () const |
| double | getFWHM () const |
| void | addMassTrace (const MassTrace &) |
| addMassTrace More... | |
| double | getMonoisotopicFeatureIntensity (bool) const |
| double | getSummedFeatureIntensity (bool) const |
| double | getMaxIntensity (bool smoothed=false) const |
| return highest apex of all isotope traces More... | |
| Size | getNumFeatPoints () const |
| std::vector< ConvexHull2D > | getConvexHulls () const |
| std::vector< OpenMS::MSChromatogram > | getChromatograms (UInt64 feature_id) const |
Private Attributes | |
| std::vector< const MassTrace * > | iso_pattern_ |
| double | feat_score_ {} |
| SignedSize | charge_ {} |
Internal structure used in FeatureFindingMetabo that keeps track of a feature hypothesis (isotope group hypothesis).
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
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| local_rt_range | float | 10.0 | RT range where to look for coeluting mass traces | |
| local_mz_range | float | 6.5 | MZ range where to look for isotopic mass traces | |
| charge_lower_bound | int | 1 | Lowest charge state to consider | |
| charge_upper_bound | int | 3 | Highest charge state to consider | |
| chrom_fwhm | float | 5.0 | Expected chromatographic peak width (in seconds). | |
| report_summed_ints | string | false | false, true | Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone. |
| enable_RT_filtering | string | true | false, true | Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data.. |
| isotope_filtering_model | string | metabolites (5% RMS) | metabolites (2% RMS), metabolites (5% RMS), peptides, none | Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device. |
| mz_scoring_13C | string | false | false, true | Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.). |
| use_smoothed_intensities | string | true | false, true | Use LOWESS intensities instead of raw intensities. |
| report_convex_hulls | string | false | false, true | Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably). |
| report_chromatograms | string | false | false, true | Adds Chromatogram for each reported feature (Output in mzml). |
| remove_single_traces | string | false | false, true | Remove unassembled traces (single traces). |
| mz_scoring_by_elements | string | false | false, true | Use the m/z range of the assumed elements to detect isotope peaks. A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C' |
| elements | string | CHNOPS | Elements assumes to be present in the sample (this influences isotope detection). |
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default constructor
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default destructor
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copy constructor
| void addMassTrace | ( | const MassTrace & | ) |
addMassTrace
| std::vector<double> getAllCentroidMZ | ( | ) | const |
| std::vector<double> getAllCentroidRT | ( | ) | const |
| std::vector<double> getAllIntensities | ( | bool | smoothed = false | ) | const |
| double getCentroidMZ | ( | ) | const |
| double getCentroidRT | ( | ) | const |
| SignedSize getCharge | ( | ) | const |
| std::vector< OpenMS::MSChromatogram > getChromatograms | ( | UInt64 | feature_id | ) | const |
| std::vector<ConvexHull2D> getConvexHulls | ( | ) | const |
| double getFWHM | ( | ) | const |
| std::vector<double> getIsotopeDistances | ( | ) | const |
| String getLabel | ( | ) | const |
| std::vector<String> getLabels | ( | ) | const |
| double getMaxIntensity | ( | bool | smoothed = false | ) | const |
return highest apex of all isotope traces
| double getMonoisotopicFeatureIntensity | ( | bool | ) | const |
| Size getNumFeatPoints | ( | ) | const |
| double getScore | ( | ) | const |
Referenced by CmpHypothesesByScore::operator()().
| Size getSize | ( | ) | const |
| double getSummedFeatureIntensity | ( | bool | ) | const |
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default |
assignment operator
| void setCharge | ( | const SignedSize & | ch | ) |
| void setScore | ( | const double & | score | ) |
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1.9.1 
