filters centroided data for peak patterns More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteringCentroided.h>
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 < MultiplexFilterResult > | filter () |
filter for patterns (generates a filter result for each of the patterns) More... | |
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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... | |
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ProgressLogger () | |
Constructor. More... | |
~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... | |
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 | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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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... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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MSExperiment< Peak1D > | exp_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< MultiplexPeakPattern > | patterns_ |
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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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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< 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
exp_picked | experimental data in centroid mode |
patterns | patterns of isotopic peaks to be searched for |
peaks_per_peptide_min | minimum number of isotopic peaks in peptides |
peaks_per_peptide_max | maximum number of isotopic peaks in peptides |
missing_peaks | flag for missing peaks |
intensity_cutoff | intensity cutoff |
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). |
std::vector<MultiplexFilterResult> filter | ( | ) |
filter for patterns (generates a filter result for each of the patterns)
returns the index of a peak at m/z (for initialisation of peak registry)
spectrum_index | index of the spectrum in exp_picked_ and boundaries_ |
mz | m/z position of the peak |
scaling | rescaling of the peak boundaries |
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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.)
pattern | pattern of isotopic peaks to be searched for |
spectrum_index | index of the spectrum in exp_picked_ and boundaries_ |
mz_shifts_actual_indices | indices of peaks corresponding to the pattern |
intensities_actual | output for the spline-interpolated intensities at the actual m/z shift positions |
peaks_found_in_all_peptides | number of isotopic peaks seen for each peptide (peaks) |
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:48 using doxygen 1.8.5 |