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OpenMS
2.8.0
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filters centroided data for peak patterns More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteringCentroided.h>
Public Member Functions | |
| MultiplexFilteringCentroided (const MSExperiment &exp_centroided, const std::vector< MultiplexIsotopicPeakPattern > &patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide") | |
| constructor More... | |
| std::vector< MultiplexFilteredMSExperiment > | filter () |
| filter for patterns (generates a filter result for each of the patterns) More... | |
 Public Member Functions inherited from MultiplexFiltering | |
| MultiplexFiltering (const MSExperiment &exp_centroided, const std::vector< MultiplexIsotopicPeakPattern > &patterns, int isotopes_per_peptide_min, int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide") | |
| constructor More... | |
| MSExperiment & | getCentroidedExperiment () |
| returns the intensity-filtered, centroided spectral data More... | |
| MSExperiment | getBlacklist () |
| returns the blacklisted, centroided peaks More... | |
| Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| virtual | ~ProgressLogger () |
| Destructor. More... | |
| ProgressLogger (const ProgressLogger &other) | |
| Copy constructor. More... | |
| ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
| void | nextProgress () const |
| increment progress by 1 (according to range begin-end) More... | |
Additional Inherited Members | |
| Public Types inherited from MultiplexFiltering | |
| typedef std::vector< std::map< int, int > > | White2Original |
| index mapping from a 'white' experiment to its original experiment More... | |
| Public Types inherited from ProgressLogger | |
| enum | LogType { CMD , GUI , NONE } |
| Possible log types. More... | |
| Protected Member Functions inherited from MultiplexFiltering | |
| void | updateWhiteMSExperiment_ () |
| construct an MS experiment from exp_centroided_ containing peaks which have not been previously blacklisted in blacklist_ More... | |
| int | checkForSignificantPeak_ (double mz, double mz_tolerance, MSExperiment::ConstIterator &it_rt, double intensity_first_peak) const |
| check for significant peak More... | |
| bool | filterPeakPositions_ (double mz, const MSExperiment::ConstIterator &it_rt_begin, const MSExperiment::ConstIterator &it_rt_band_begin, const MSExperiment::ConstIterator &it_rt_band_end, const MultiplexIsotopicPeakPattern &pattern, MultiplexFilteredPeak &peak) const |
| check if there are enough peaks in the RT band to form the pattern More... | |
| void | blacklistPeak_ (const MultiplexFilteredPeak &peak) |
| blacklist this peak More... | |
| void | blacklistPeak_ (const MultiplexFilteredPeak &peak, unsigned pattern_idx) |
| blacklist this peak More... | |
| bool | filterAveragineModel_ (const MultiplexIsotopicPeakPattern &pattern, const MultiplexFilteredPeak &peak) const |
| check if the satellite peaks conform with the averagine model More... | |
| bool | filterPeptideCorrelation_ (const MultiplexIsotopicPeakPattern &pattern, const MultiplexFilteredPeak &peak) const |
| check if corresponding satellite peaks of different peptides show a good correlation More... | |
| Static Protected Member Functions inherited from ProgressLogger | |
| static String | logTypeToFactoryName_ (LogType type) |
| Return the name of the factory product used for this log type. More... | |
| Protected Attributes inherited from MultiplexFiltering | |
| MSExperiment | exp_centroided_ |
| centroided experimental data More... | |
| std::vector< std::vector< int > > | blacklist_ |
| auxiliary structs for blacklisting More... | |
| MSExperiment | exp_centroided_white_ |
| "white" centroided experimental data More... | |
| White2Original | exp_centroided_mapping_ |
| mapping of peak indices from a 'white' experiment exp_centroided_white_ to its original experiment exp_centroided_ More... | |
| std::vector< MultiplexIsotopicPeakPattern > | patterns_ |
| list of peak patterns More... | |
| size_t | isotopes_per_peptide_min_ |
| minimum number of isotopic peaks per peptide More... | |
| size_t | isotopes_per_peptide_max_ |
| maximum number of isotopic peaks per peptide More... | |
| double | intensity_cutoff_ |
| intensity cutoff More... | |
| double | rt_band_ |
| RT range used for filtering. More... | |
| double | mz_tolerance_ |
| m/z shift tolerance More... | |
| bool | mz_tolerance_unit_in_ppm_ |
| unit for m/z shift tolerance (ppm - true, Da - false) More... | |
| double | peptide_similarity_ |
| peptide similarity More... | |
| double | averagine_similarity_ |
| averagine similarity More... | |
| double | averagine_similarity_scaling_ |
| averagine similarity scaling More... | |
| String | averagine_type_ |
| type of averagine to use More... | |
| Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| time_t | last_invoke_ |
| ProgressLoggerImpl * | current_logger_ |
| Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
filters centroided data for peak patterns
The algorithm searches for patterns of multiple peptides in the data. The peptides appear as characteristic patterns of isotopic peaks in MS1 spectra. We search the centroided data for such patterns. For each peak pattern the algorithm generates a filter result.
| MultiplexFilteringCentroided | ( | const MSExperiment & | exp_centroided, |
| const std::vector< MultiplexIsotopicPeakPattern > & | patterns, | ||
| int | isotopes_per_peptide_min, | ||
| int | isotopes_per_peptide_max, | ||
| double | intensity_cutoff, | ||
| double | rt_band, | ||
| double | mz_tolerance, | ||
| bool | mz_tolerance_unit, | ||
| double | peptide_similarity, | ||
| double | averagine_similarity, | ||
| double | averagine_similarity_scaling, | ||
| String | averagine_type = "peptide" |
||
| ) |
constructor
| exp_centroided | experimental data in centroid mode |
| patterns | patterns of isotopic peaks to be searched for |
| isotopes_per_peptide_min | minimum number of isotopic peaks in peptides |
| isotopes_per_peptide_max | maximum number of isotopic peaks in peptides |
| intensity_cutoff | intensity cutoff |
| rt_band | RT range for filtering |
| mz_tolerance | error margin in m/z for matching expected patterns to experimental data |
| mz_tolerance_unit | unit for mz_tolerance, ppm (true), Da (false) |
| peptide_similarity | similarity score for two peptides in the same multiplet |
| averagine_similarity | similarity score for peptide isotope pattern and averagine model |
| averagine_similarity_scaling | scaling factor x for the averagine similarity parameter p when detecting peptide singlets. With p' = p + x(1-p). |
| averagine_type | The averagine model to use, current options are RNA DNA or peptide. |
| std::vector<MultiplexFilteredMSExperiment> filter | ( | ) |
filter for patterns (generates a filter result for each of the patterns)
1.9.1
