OpenMS
2.4.0
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The PeakPickerMRM finds peaks a single chromatogram. More...
#include <OpenMS/ANALYSIS/OPENSWATH/PeakPickerMRM.h>
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 ¶m) |
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... | |
The PeakPickerMRM finds peaks a single chromatogram.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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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. |
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sgolay_polynomial_order | int | 3 | Order of the polynomial that is fitted. | |
gauss_width | float | 50 | 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 | 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 | min: 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 | Signal to noise window length. | |
sn_bin_count | int | 30 | Signal to noise bin count. | |
write_sn_log_messages | string | true | 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). |
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.
PeakPickerMRM | ( | ) |
Constructor.
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inlineoverride |
Destructor.
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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.
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Compute peak area (peak integration)
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Assignment operator is protected for algorithm.
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
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
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Helper function to remove overlapping peaks in a single Chromatogram.
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Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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Width of the Gaussian smoothing.
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Temporary vector to hold the integrated intensities.
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Temporary vector to hold the peak left widths.
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Peak picker method.
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Forced peak with.
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Whether to resolve overlapping peaks.
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Temporary vector to hold the peak right widths.
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Frame length for the SGolay smoothing.
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Polynomial order for the SGolay smoothing.
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Signal to noise threshold.
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Signal to noise bin count.
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Signal to noise window length.
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Whether to use Gaussian smoothing.
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Whether to write out log messages of the SN estimator.