| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
PeakPickerMRM Class Reference

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

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

Inheritance diagram for PeakPickerMRM:

## Public Types

enum | FLOATINDICES { IDX_FWHM = 0, IDX_ABUNDANCE = 1, IDX_LEFTBORDER = 2, IDX_RIGHTBORDER = 3, SIZE_OF_FLOATINDICES }
| indices into FloatDataArrays of resulting picked chromatograms More...

## Public Member Functions

void | pickChromatogram (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
| Finds peaks in a single chromatogram and annotates left/right borders. More...
void | pickChromatogram (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom, MSChromatogram &smoothed_chrom)
| Finds peaks in a single chromatogram and annotates left/right borders. More...
| PeakPickerMRM ()
| Constructor. More...
| ~PeakPickerMRM () override
| 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 DefaultParamHandler & | operator= (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 Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () 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 MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
void | pickChromatogram_ (const MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
void | integratePeaks_ (const MSChromatogram &chromatogram)
| Compute peak area (peak integration) More...
Size | findClosestPeak_ (const MSChromatogram &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 MSChromatogram &chromatogram, MSChromatogram &picked_chrom)
| Helper function to remove overlapping peaks in a single Chromatogram. More...
void | updateMembers_ () override
| Synchronize members with param class. More...
PeakPickerMRM & | operator= (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_
| Frame length for the SGolay smoothing. More...
UInt | sgolay_polynomial_order_
| Polynomial order for the SGolay smoothing. More...
double | gauss_width_
| Width of the Gaussian smoothing. More...
bool | use_gauss_
| Whether to use Gaussian smoothing. More...
bool | remove_overlapping_
| Whether to resolve overlapping peaks. More...
double | peak_width_
| Forced peak with. More...
double | signal_to_noise_
| Signal to noise threshold. More...
double | sn_win_len_
| Signal to noise window length. More...
UInt | sn_bin_count_
| Signal to noise bin count. More...
bool | write_sn_log_messages_
| Whether to write out log messages of the SN estimator. More...
String | method_
| Peak picker method. More...
std::vector< double > | integrated_intensities_
| Temporary vector to hold the integrated intensities. More...
std::vector< int > | left_width_
| Temporary vector to hold the peak left widths. More...
std::vector< int > | right_width_
| Temporary vector to hold the peak right widths. More...
PeakPickerHiRes | pp_
SavitzkyGolayFilter | sgolay_
GaussFilter | gauss_
SignalToNoiseEstimatorMedian< MSChromatogram > | snt_
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< String > | subsections_
| 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:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
sgolay_frame_length | int | 15 |  | 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 | int | 3 |  | Order of the polynomial that is fitted.
gauss_width | float | 50.0 |  | Gaussian width in seconds, estimated peak size.
use_gauss | string | true | false, true | Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
peak_width | float | -1.0 |  | 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 | float | 1.0 | min: 0.0 | Signal-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 | float | 1000.0 |  | Signal to noise window length.
sn_bin_count | int | 30 |  | Signal to noise bin count.
write_sn_log_messages | string | false | true, false | Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
remove_overlapping_peaks | string | false | false, true | Try to remove overlapping peaks during peak picking
method | string | corrected | legacy, corrected, crawdad | Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram).

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

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 Enumeration Documentation

## ◆ FLOATINDICES

enum FLOATINDICES

indices into FloatDataArrays of resulting picked chromatograms

Enumerator
IDX_FWHM |
IDX_ABUNDANCE |
IDX_LEFTBORDER |
IDX_RIGHTBORDER |
SIZE_OF_FLOATINDICES |

## Constructor & Destructor Documentation

## ◆ PeakPickerMRM()

PeakPickerMRM | ( |  | ) |

Constructor.

## ◆ ~PeakPickerMRM()

~PeakPickerMRM | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ findClosestPeak_()

Size findClosestPeak_ | ( | const MSChromatogram & | 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.

## ◆ integratePeaks_()

void integratePeaks_ | ( | const MSChromatogram & | chromatogram | ) |

protected

Compute peak area (peak integration)

## ◆ operator=()

PeakPickerMRM& operator= | ( | const PeakPickerMRM & | rhs | ) |

protected

Assignment operator is protected for algorithm.

## ◆ pickChromatogram() [1/2]

void pickChromatogram | ( | const MSChromatogram & | chromatogram,
|  | MSChromatogram & | 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

## ◆ pickChromatogram() [2/2]

void pickChromatogram | ( | const MSChromatogram & | chromatogram,
|  | MSChromatogram & | picked_chrom,
|  | MSChromatogram & | smoothed_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 and a smoothed chromatogram

## ◆ pickChromatogram_()

void pickChromatogram_ | ( | const MSChromatogram & | chromatogram,
|  | MSChromatogram & | picked_chrom
| ) |  |

protected

## ◆ pickChromatogramCrawdad_()

void pickChromatogramCrawdad_ | ( | const MSChromatogram & | chromatogram,
|  | MSChromatogram & | picked_chrom
| ) |  |

protected

## ◆ removeOverlappingPeaks_()

void removeOverlappingPeaks_ | ( | const MSChromatogram & | chromatogram,
|  | MSChromatogram & | picked_chrom
| ) |  |

protected

Helper function to remove overlapping peaks in a single Chromatogram.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ gauss_

GaussFilter gauss_

protected

## ◆ gauss_width_

double gauss_width_

protected

Width of the Gaussian smoothing.

## ◆ integrated_intensities_

std::vector<double> integrated_intensities_

protected

Temporary vector to hold the integrated intensities.

## ◆ left_width_

std::vector<int> left_width_

protected

Temporary vector to hold the peak left widths.

## ◆ method_

String method_

protected

Peak picker method.

## ◆ peak_width_

double peak_width_

protected

Forced peak with.

## ◆ pp_

PeakPickerHiRes pp_

protected

## ◆ remove_overlapping_

bool remove_overlapping_

protected

Whether to resolve overlapping peaks.

## ◆ right_width_

std::vector<int> right_width_

protected

Temporary vector to hold the peak right widths.

## ◆ sgolay_

SavitzkyGolayFilter sgolay_

protected

## ◆ sgolay_frame_length_

UInt sgolay_frame_length_

protected

Frame length for the SGolay smoothing.

## ◆ sgolay_polynomial_order_

UInt sgolay_polynomial_order_

protected

Polynomial order for the SGolay smoothing.

## ◆ signal_to_noise_

double signal_to_noise_

protected

Signal to noise threshold.

## ◆ sn_bin_count_

UInt sn_bin_count_

protected

Signal to noise bin count.

## ◆ sn_win_len_

double sn_win_len_

protected

Signal to noise window length.

## ◆ snt_

SignalToNoiseEstimatorMedian<MSChromatogram > snt_

protected

## ◆ use_gauss_

bool use_gauss_

protected

Whether to use Gaussian smoothing.

## ◆ write_sn_log_messages_

bool write_sn_log_messages_

protected

Whether to write out log messages of the SN estimator.