FIAMSDataProcessor
- class pyopenms.FIAMSDataProcessor
Bases:
objectCython implementation of _FIAMSDataProcessor
- Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1FIAMSDataProcessor.html
– Inherits from [‘DefaultParamHandler’]
ADD PYTHON DOCUMENTATION HERE
- __init__()
Cython signature: void FIAMSDataProcessor() Data processing for FIA-MS data
Cython signature: void FIAMSDataProcessor(FIAMSDataProcessor &)
Methods
Cython signature: void FIAMSDataProcessor()
Cython signature: FeatureMap convertToFeatureMap(MSSpectrum & input_)
Cython signature: MSSpectrum extractPeaks(MSSpectrum & input_)
Cython signature: Param getDefaults() Returns the default parameters
Cython signature: String getName() Returns the name
Cython signature: Param getParameters() Returns the parameters
Cython signature: libcpp_vector[String] getSubsections()
Cython signature: bool run(MSExperiment & experiment, float & n_seconds, MzTab & output, bool load_cached_spectrum)
Cython signature: void setName(const String &) Sets the name
Cython signature: void setParameters(Param & param) Sets the parameters
Cython signature: MSSpectrum trackNoise(MSSpectrum & input_)
- convertToFeatureMap()
Cython signature: FeatureMap convertToFeatureMap(MSSpectrum & input_)
- Parameters
input – Input a picked spectrum
- Returns
A feature map with the peaks converted to features and polarity from the parameters
- Parameters
input – Input a picked spectrum
- Returns
A spectrum object storing logSN information
- extractPeaks()
Cython signature: MSSpectrum extractPeaks(MSSpectrum & input_)
- Parameters
input – Input vector of spectra
- Returns
A spectrum with picked peaks
- Parameters
input – Input a picked spectrum
- Returns
A feature map with the peaks converted to features and polarity from the parameters
- Parameters
input – Input a picked spectrum
- Returns
A spectrum object storing logSN information
- getDefaults()
Cython signature: Param getDefaults() Returns the default parameters
- getName()
Cython signature: String getName() Returns the name
- getParameters()
Cython signature: Param getParameters() Returns the parameters
- getSubsections()
Cython signature: libcpp_vector[String] getSubsections()
- run()
Cython signature: bool run(MSExperiment & experiment, float & n_seconds, MzTab & output, bool load_cached_spectrum)
The workflow steps are: - the time axis of the experiment is cut to the interval from 0 to n_seconds - the spectra are summed into one along the time axis with the bin size determined by mz and instrument resolution - data is smoothed by applying the Savitzky-Golay filter - peaks are picked - the accurate mass search for all the picked peaks is performed
- setName()
Cython signature: void setName(const String &) Sets the name
- setParameters()
Cython signature: void setParameters(Param & param) Sets the parameters