MRMFeatureFinderScoring#
- class pyopenms.MRMFeatureFinderScoring#
Bases:
object
Cython implementation of _MRMFeatureFinderScoring
- Original C++ documentation is available here
– Inherits from [‘DefaultParamHandler’, ‘ProgressLogger’]
- __init__(self) None #
Methods
__init__
(self)endProgress
(self)Ends the progress display
getDefaults
(self)Returns the default parameters
getLogType
(self)Returns the type of progress log being used
getName
(self)Returns the name
getParameters
(self)Returns the parameters
getSubsections
(self)nextProgress
(self)Increment progress by 1 (according to range begin-end)
pickExperiment
(self, chromatograms, output, ...)Pick features in one experiment containing chromatogram
prepareProteinPeptideMaps_
(self, transition_exp)Prepares the internal mappings of peptides and proteins
scorePeakgroups
(self, transition_group, ...)Score all peak groups of a transition group
setLogType
(self, in_0)Sets the progress log that should be used.
Overload:
setName
(self, in_0)Sets the name
setParameters
(self, param)Sets the parameters
setProgress
(self, value)Sets the current progress
setStrictFlag
(self, flag)startProgress
(self, begin, end, label)- endProgress(self) None #
Ends the progress display
- getLogType(self) int #
Returns the type of progress log being used
- getSubsections(self) List[bytes] #
- nextProgress(self) None #
Increment progress by 1 (according to range begin-end)
- pickExperiment(self, chromatograms: MSExperiment, output: FeatureMap, transition_exp_: TargetedExperiment, trafo: TransformationDescription, swath_map: MSExperiment) None #
Pick features in one experiment containing chromatogram
Function for for wrapping in Python, only uses OpenMS datastructures and does not return the map
- Parameters:
chromatograms – The input chromatograms
output – The output features with corresponding scores
transition_exp – The transition list describing the experiment
trafo – Optional transformation of the experimental retention time to the normalized retention time space used in the transition list
swath_map – Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted
- prepareProteinPeptideMaps_(self, transition_exp: LightTargetedExperiment) None #
Prepares the internal mappings of peptides and proteins
Calling this method _is_ required before calling scorePeakgroups
- Parameters:
transition_exp – The transition list describing the experiment
- scorePeakgroups(self, transition_group: LightMRMTransitionGroupCP, trafo: TransformationDescription, swath_maps: List[SwathMap], output: FeatureMap, ms1only: bool) None #
Score all peak groups of a transition group
Iterate through all features found along the chromatograms of the transition group and score each one individually
- Parameters:
transition_group – The MRMTransitionGroup to be scored (input)
trafo – Optional transformation of the experimental retention time to the normalized retention time space used in thetransition list
swath_maps – Optional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available
output – The output features with corresponding scores (the found features will be added to this FeatureMap)
ms1only – Whether to only do MS1 scoring and skip all MS2 scoring
- setLogType(self, in_0: int) None #
Sets the progress log that should be used. The default type is NONE!
- setMS1Map()#
Overload:
- setMS1Map(self, ms1_map: SpectrumAccessOpenMS) None
Overload:
- setMS1Map(self, ms1_map: SpectrumAccessOpenMSCached) None
- setProgress(self, value: int) None #
Sets the current progress
- setStrictFlag(self, flag: bool) None #