FeatureFinderAlgorithmMetaboIdent#
- class pyopenms.FeatureFinderAlgorithmMetaboIdent#
Bases:
objectCython implementation of _FeatureFinderAlgorithmMetaboIdent
- Original C++ documentation is available here
– Inherits from [‘DefaultParamHandler’]
Perform targeted feature extraction of compounds provided as table and stores them in features
The algorithms detects quantitative features in MS1 data for a list of targets, typically small molecule/metabolite identifications Internally, it uses algorithms for targeted data analysis from the OpenSWATH pipeline In the simplest case, only CompoundName, SumFormula, Charge and RetentionTime need to be given, all other values may be zero Every combination of compound (mass), RT and charge defines one target for feature detection Output: The main output is a feature map of detected features, with annotations in meta data entries Additional outputs are the extracted chromatograms/peak groups, the assay in TraML compatible format, and transformations that contain the error between provided and observed peaks
Usage:
- __init__(self) None#
Methods
__init__(self)getChromatograms(self)Retrieves chromatograms (empty if run was not executed)
getDefaults(self)Returns the default parameters
getLibrary(self)Retrieves the assay library (e.g., to store as TraML, empty if run was not executed)
getMSData(self)Returns spectra
getNShared(self)Retrieves number of features with shared identifications
getName(self)Returns the name
getParameters(self)Returns the parameters
getSubsections(self)getTransformations(self)Retrieves deviations between provided coordinates and extacted ones (e.g., to store as TrafoXML or for plotting)
run(self, metaboIdentTable, features, ...)Run feature extraction.
setMSData(self, input)Sets spectra
setName(self, in_0)Sets the name
setParameters(self, param)Sets the parameters
- getChromatograms(self) MSExperiment#
Retrieves chromatograms (empty if run was not executed)
- getLibrary(self) TargetedExperiment#
Retrieves the assay library (e.g., to store as TraML, empty if run was not executed)
- getMSData(self) MSExperiment#
Returns spectra
Retrieves number of features with shared identifications
- getSubsections(self) List[bytes]#
- getTransformations(self) TransformationDescription#
Retrieves deviations between provided coordinates and extacted ones (e.g., to store as TrafoXML or for plotting)
- run(self, metaboIdentTable: List[FeatureFinderMetaboIdentCompound], features: FeatureMap, spectra_path: bytes | str | String) None#
Run feature extraction. spectra_path get’s annotated as primaryMSRunPath in the resulting feature map.
- setMSData(self, input: MSExperiment) None#
Sets spectra