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MultiplexFilteringCentroided Class Reference

filters centroided data for peak patterns More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteringCentroided.h>

Inheritance diagram for MultiplexFilteringCentroided:
MultiplexFiltering ProgressLogger

Public Member Functions

 MultiplexFilteringCentroided (const MSExperiment< Peak1D > &exp_picked, const std::vector< MultiplexPeakPattern > patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling)
 constructor More...
 
std::vector< MultiplexFilterResultfilter ()
 filter for patterns (generates a filter result for each of the patterns) More...
 
- Public Member Functions inherited from MultiplexFiltering
 MultiplexFiltering (const MSExperiment< Peak1D > &exp_picked, const std::vector< MultiplexPeakPattern > patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling)
 constructor More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (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...
 

Private Member Functions

int nonLocalIntensityFilter (MultiplexPeakPattern pattern, int spectrum_index, const std::vector< int > &mz_shifts_actual_indices, std::vector< double > &intensities_actual, int peaks_found_in_all_peptides) const
 non-local intensity filter More...
 
int getPeakIndex (int spectrum_index, double mz, double scaling) const
 returns the index of a peak at m/z (for initialisation of peak registry) More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Member Functions inherited from MultiplexFiltering
int positionsAndBlacklistFilter (MultiplexPeakPattern pattern, int spectrum, std::vector< double > peak_position, int peak, std::vector< double > &mz_shifts_actual, std::vector< int > &mz_shifts_actual_indices) const
 position and blacklist filter More...
 
bool monoIsotopicPeakIntensityFilter (MultiplexPeakPattern pattern, int spectrum_index, const std::vector< int > &mz_shifts_actual_indices) const
 mono-isotopic peak intensity filter More...
 
bool zerothPeakFilter (MultiplexPeakPattern pattern, const std::vector< double > &intensities_actual) const
 zeroth peak filter More...
 
bool peptideSimilarityFilter (MultiplexPeakPattern pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline) const
 peptide similarity filter More...
 
bool averagineSimilarityFilter (MultiplexPeakPattern pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline, double mz) const
 averagine similarity filter More...
 
void blacklistPeaks (MultiplexPeakPattern pattern, int spectrum, const std::vector< int > &mz_shifts_actual_indices, int peaks_found_in_all_peptides_spline)
 blacklist peaks More...
 
int getPeakIndex (std::vector< double > peak_position, int start, double mz, double scaling) const
 returns the index of a peak at m/z (finds not only a valid peak, i.e. within certain m/z deviation, but the best of the valid peaks) More...
 
double getPatternSimilarity (std::vector< double > pattern1, std::vector< double > pattern2) const
 returns similarity of two isotope patterns (simple Pearson correlation coefficient) More...
 
double getAveragineSimilarity (std::vector< double > pattern, double m) const
 returns similarity of an isotope pattern and an averagine pattern at mass m 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< Peak1Dexp_picked_
 centroided experimental data More...
 
std::vector< std::vector< PeakReference > > registry_
 auxiliary structs for navigation and blacklisting More...
 
std::vector< std::vector< BlackListEntry > > blacklist_
 
std::vector< MultiplexPeakPatternpatterns_
 list of peak patterns More...
 
int peaks_per_peptide_min_
 minimum number of isotopic peaks per peptide More...
 
int peaks_per_peptide_max_
 maximum number of isotopic peaks per peptide More...
 
bool missing_peaks_
 flag for missing peaks More...
 
double intensity_cutoff_
 intensity cutoff More...
 
double mz_tolerance_
 m/z shift tolerance More...
 
bool mz_tolerance_unit_
 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

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.

See also
MultiplexPeakPattern
MultiplexFilterResult
MultiplexFiltering

Constructor & Destructor Documentation

MultiplexFilteringCentroided ( const MSExperiment< Peak1D > &  exp_picked,
const std::vector< MultiplexPeakPattern patterns,
int  peaks_per_peptide_min,
int  peaks_per_peptide_max,
bool  missing_peaks,
double  intensity_cutoff,
double  mz_tolerance,
bool  mz_tolerance_unit,
double  peptide_similarity,
double  averagine_similarity,
double  averagine_similarity_scaling 
)

constructor

Parameters
exp_pickedexperimental data in centroid mode
patternspatterns of isotopic peaks to be searched for
peaks_per_peptide_minminimum number of isotopic peaks in peptides
peaks_per_peptide_maxmaximum number of isotopic peaks in peptides
missing_peaksflag for missing peaks
intensity_cutoffintensity cutoff
mz_toleranceerror margin in m/z for matching expected patterns to experimental data
mz_tolerance_unitunit for mz_tolerance, ppm (true), Da (false)
peptide_similaritysimilarity score for two peptides in the same multiplet
averagine_similaritysimilarity score for peptide isotope pattern and averagine model
averagine_similarity_scalingscaling factor x for the averagine similarity parameter p when detecting peptide singlets. With p' = p + x(1-p).

Member Function Documentation

std::vector<MultiplexFilterResult> filter ( )

filter for patterns (generates a filter result for each of the patterns)

See also
MultiplexPeakPattern, MultiplexFilterResult
int getPeakIndex ( int  spectrum_index,
double  mz,
double  scaling 
) const
private

returns the index of a peak at m/z (for initialisation of peak registry)

Parameters
spectrum_indexindex of the spectrum in exp_picked_ and boundaries_
mzm/z position of the peak
scalingrescaling of the peak boundaries
Returns
index of the peak in spectrum
int nonLocalIntensityFilter ( MultiplexPeakPattern  pattern,
int  spectrum_index,
const std::vector< int > &  mz_shifts_actual_indices,
std::vector< double > &  intensities_actual,
int  peaks_found_in_all_peptides 
) const
private

non-local intensity filter

Checks if the intensities at the pattern positions are above the intensity cutoff. We check not only at m/z but at all pattern positions i.e. non-locally. (In filter 1 we checked that peaks do exist at these positions. In filter 2 we checked that the mono-isotopic peak intensities are above the threshold.)

Parameters
patternpattern of isotopic peaks to be searched for
spectrum_indexindex of the spectrum in exp_picked_ and boundaries_
mz_shifts_actual_indicesindices of peaks corresponding to the pattern
intensities_actualoutput for the spline-interpolated intensities at the actual m/z shift positions
peaks_found_in_all_peptidesnumber of isotopic peaks seen for each peptide (peaks)
Returns
number of isotopic peaks seen for each peptide (profile)

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:29 using doxygen 1.8.11