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PeakPickerMRM Class Reference

The PeakPickerMRM finds peaks a single chromatogram. More...

#include <OpenMS/ANALYSIS/OPENSWATH/PeakPickerMRM.h>

Inheritance diagram for PeakPickerMRM:
DefaultParamHandler

Public Types

typedef MSSpectrum< ChromatogramPeakRichPeakChromatogram
 

Public Member Functions

void pickChromatogram (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
 Finds peaks in a single chromatogram and annotates left/right borders. More...
 
 PeakPickerMRM ()
 Constructor. More...
 
 ~PeakPickerMRM ()
 Destructor. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Protected Member Functions

void pickChromatogramCrawdad_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
 
void pickChromatogram_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
 
void integratePeaks_ (const RichPeakChromatogram &chromatogram)
 Compute peak area (peak integration) More...
 
Size findClosestPeak_ (const RichPeakChromatogram &chromatogram, double target_rt, Size current_peak=0)
 Helper function to find the closest peak in a chromatogram to "target_rt". More...
 
void removeOverlappingPeaks_ (const RichPeakChromatogram &chromatogram, RichPeakChromatogram &picked_chrom)
 Helper function to remove overlapping peaks in a single Chromatogram. More...
 
void updateMembers_ ()
 Synchronize members with param class. More...
 
PeakPickerMRMoperator= (const PeakPickerMRM &rhs)
 Assignment operator is protected for algorithm. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

UInt sgolay_frame_length_
 
UInt sgolay_polynomial_order_
 
double gauss_width_
 
bool use_gauss_
 
bool remove_overlapping_
 
double peak_width_
 
double signal_to_noise_
 
double sn_win_len_
 
UInt sn_bin_count_
 
String method_
 
std::vector< doubleintegrated_intensities_
 
std::vector< int > left_width_
 
std::vector< int > right_width_
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

The PeakPickerMRM finds peaks a single chromatogram.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
sgolay_frame_length int15  The number of subsequent data points used for smoothing.
This number has to be uneven. If it is not, 1 will be added.
sgolay_polynomial_order int3  Order of the polynomial that is fitted.
gauss_width float50  Gaussian width in seconds, estimated peak size.
use_gauss stringtrue  Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
peak_width float40  Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
signal_to_noise float1 min: 0Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
sn_win_len float1000  Signal to noise window length.
sn_bin_count int30  Signal to noise bin count.
remove_overlapping_peaks stringfalse false, trueTry to remove overlapping peaks during peak picking
method stringlegacy legacy, corrected, crawdadWhich method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad).

Note:

It uses the PeakPickerHiRes internally to find interesting seed candidates. These candidates are then expanded and a right/left border of the peak is searched. Additionally, overlapping peaks can be removed.

Member Typedef Documentation

Constructor & Destructor Documentation

Constructor.

~PeakPickerMRM ( )
inline

Destructor.

Member Function Documentation

Size findClosestPeak_ ( const RichPeakChromatogram chromatogram,
double  target_rt,
Size  current_peak = 0 
)
protected

Helper function to find the closest peak in a chromatogram to "target_rt".

The search will start from the index current_peak, so the function is assuming the closest peak is to the right of current_peak.

It will return the index of the closest peak in the chromatogram.

void integratePeaks_ ( const RichPeakChromatogram chromatogram)
protected

Compute peak area (peak integration)

PeakPickerMRM& operator= ( const PeakPickerMRM rhs)
protected

Assignment operator is protected for algorithm.

void pickChromatogram ( const RichPeakChromatogram chromatogram,
RichPeakChromatogram picked_chrom 
)

Finds peaks in a single chromatogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked chromatogram

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

void pickChromatogram_ ( const RichPeakChromatogram chromatogram,
RichPeakChromatogram picked_chrom 
)
protected
void pickChromatogramCrawdad_ ( const RichPeakChromatogram chromatogram,
RichPeakChromatogram picked_chrom 
)
protected
void removeOverlappingPeaks_ ( const RichPeakChromatogram chromatogram,
RichPeakChromatogram picked_chrom 
)
protected

Helper function to remove overlapping peaks in a single Chromatogram.

void updateMembers_ ( )
protectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

double gauss_width_
protected
std::vector<double> integrated_intensities_
protected
std::vector<int> left_width_
protected
String method_
protected
double peak_width_
protected
bool remove_overlapping_
protected
std::vector<int> right_width_
protected
UInt sgolay_frame_length_
protected
UInt sgolay_polynomial_order_
protected
double signal_to_noise_
protected
UInt sn_bin_count_
protected
double sn_win_len_
protected
bool use_gauss_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:14:01 using doxygen 1.8.9.1