Kernel_MassTrace

class pyopenms.Kernel_MassTrace

Bases: object

Cython implementation of _Kernel_MassTrace

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1Kernel_MassTrace.html

__init__()

Cython signature: void Kernel_MassTrace()
Cython signature: void Kernel_MassTrace(Kernel_MassTrace &)
Cython signature: void Kernel_MassTrace(const libcpp_vector[Peak2D] & trace_peaks)

Methods

`__init__`	Cython signature: void Kernel_MassTrace()
`computeFwhmArea`	Cython signature: double computeFwhmArea()
`computeFwhmAreaSmooth`	Cython signature: double computeFwhmAreaSmooth() Computes chromatographic peak area within the FWHM range.
`computePeakArea`	Cython signature: double computePeakArea() Sums intensities of all peaks in the mass trace
`computeSmoothedPeakArea`	Cython signature: double computeSmoothedPeakArea() Sums all non-negative (smoothed!) intensities in the mass trace
`estimateFWHM`	Cython signature: size_t estimateFWHM(bool) Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)
`findMaxByIntPeak`	Cython signature: size_t findMaxByIntPeak(bool) Returns the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities)
`getAverageMS1CycleTime`	Cython signature: double getAverageMS1CycleTime() Returns average scan time of mass trace
`getCentroidMZ`	Cython signature: double getCentroidMZ() Returns the centroid m/z
`getCentroidRT`	Cython signature: double getCentroidRT() Returns the centroid RT
`getCentroidSD`	Cython signature: double getCentroidSD() Returns the centroid SD
`getConvexhull`	Cython signature: ConvexHull2D getConvexhull() Returns the mass trace's convex hull
`getFWHM`	Cython signature: double getFWHM() Returns FWHM
`getFWHMborders`	Cython signature: libcpp_pair[size_t,size_t] getFWHMborders() Returns FWHM boarders
`getIntensity`	Cython signature: double getIntensity(bool) Returns the intensity
`getLabel`	Cython signature: String getLabel() Returns label of mass trace
`getMaxIntensity`	Cython signature: double getMaxIntensity(bool) Returns the max intensity
`getQuantMethod`	Cython signature: MT_QUANTMETHOD getQuantMethod() Check if area or median is used for quantification
`getSize`	Cython signature: size_t getSize() Returns the number of peaks contained in the mass trace
`getSmoothedIntensities`	Cython signature: libcpp_vector[double] getSmoothedIntensities() Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)
`getTraceLength`	Cython signature: double getTraceLength() Returns the length of the trace (as difference in RT)
`setCentroidSD`	Cython signature: void setCentroidSD(double & tmp_sd)
`setLabel`	Cython signature: void setLabel(String label) Sets label of mass trace
`setQuantMethod`	Cython signature: void setQuantMethod(MT_QUANTMETHOD method) Determine if area or median is used for quantification
`setSmoothedIntensities`	Cython signature: void setSmoothedIntensities(libcpp_vector[double] & db_vec) Sets smoothed intensities (smoothing is done externally, e.g.
`updateMeanMZ`	Cython signature: void updateMeanMZ() Compute & update centroid m/z as mean of m/z values
`updateMedianMZ`	Cython signature: void updateMedianMZ() Compute & update centroid m/z as median of m/z values
`updateMedianRT`	Cython signature: void updateMedianRT() Compute & update centroid RT as median position of intensities
`updateSmoothedMaxRT`	Cython signature: void updateSmoothedMaxRT()
`updateSmoothedWeightedMeanRT`	Cython signature: void updateSmoothedWeightedMeanRT()
`updateWeightedMZsd`	Cython signature: void updateWeightedMZsd()
`updateWeightedMeanMZ`	Cython signature: void updateWeightedMeanMZ() Compute & update centroid m/z as weighted mean of m/z values
`updateWeightedMeanRT`	Cython signature: void updateWeightedMeanRT() Compute & update centroid RT as a intensity-weighted mean of RTs

Attributes

fwhm_mz_avg

computeFwhmArea(): Cython signature: double computeFwhmArea()

computeFwhmAreaSmooth(): Cython signature: double computeFwhmAreaSmooth() Computes chromatographic peak area within the FWHM range.

computePeakArea(): Cython signature: double computePeakArea() Sums intensities of all peaks in the mass trace

computeSmoothedPeakArea(): Cython signature: double computeSmoothedPeakArea() Sums all non-negative (smoothed!) intensities in the mass trace

estimateFWHM(): Cython signature: size_t estimateFWHM(bool) Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)

findMaxByIntPeak(): Cython signature: size_t findMaxByIntPeak(bool) Returns the index of the mass trace’s highest peak within the MassTrace container (based either on raw or smoothed intensities)

fwhm_mz_avg

getAverageMS1CycleTime(): Cython signature: double getAverageMS1CycleTime() Returns average scan time of mass trace

getCentroidMZ(): Cython signature: double getCentroidMZ() Returns the centroid m/z

getCentroidRT(): Cython signature: double getCentroidRT() Returns the centroid RT

getCentroidSD(): Cython signature: double getCentroidSD() Returns the centroid SD

getConvexhull(): Cython signature: ConvexHull2D getConvexhull() Returns the mass trace’s convex hull

getFWHM(): Cython signature: double getFWHM() Returns FWHM

getFWHMborders(): Cython signature: libcpp_pair[size_t,size_t] getFWHMborders() Returns FWHM boarders

getIntensity(): Cython signature: double getIntensity(bool) Returns the intensity

getLabel(): Cython signature: String getLabel() Returns label of mass trace

getMaxIntensity(): Cython signature: double getMaxIntensity(bool) Returns the max intensity

getQuantMethod(): Cython signature: MT_QUANTMETHOD getQuantMethod() Check if area or median is used for quantification

getSize(): Cython signature: size_t getSize() Returns the number of peaks contained in the mass trace

getSmoothedIntensities(): Cython signature: libcpp_vector[double] getSmoothedIntensities() Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)

getTraceLength(): Cython signature: double getTraceLength() Returns the length of the trace (as difference in RT)

setCentroidSD(): Cython signature: void setCentroidSD(double & tmp_sd)

setLabel(): Cython signature: void setLabel(String label) Sets label of mass trace

setQuantMethod(): Cython signature: void setQuantMethod(MT_QUANTMETHOD method) Determine if area or median is used for quantification

setSmoothedIntensities(): Cython signature: void setSmoothedIntensities(libcpp_vector[double] & db_vec) Sets smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing)

updateMeanMZ(): Cython signature: void updateMeanMZ() Compute & update centroid m/z as mean of m/z values

updateMedianMZ(): Cython signature: void updateMedianMZ() Compute & update centroid m/z as median of m/z values

updateMedianRT(): Cython signature: void updateMedianRT() Compute & update centroid RT as median position of intensities

updateSmoothedMaxRT(): Cython signature: void updateSmoothedMaxRT()

updateSmoothedWeightedMeanRT(): Cython signature: void updateSmoothedWeightedMeanRT()

updateWeightedMZsd()

Cython signature: void updateWeightedMZsd()

Make sure to call update(Weighted)(Mean|Median)MZ() first! <br> use getCentroidSD() to get result

updateWeightedMeanMZ(): Cython signature: void updateWeightedMeanMZ() Compute & update centroid m/z as weighted mean of m/z values

updateWeightedMeanRT(): Cython signature: void updateWeightedMeanRT() Compute & update centroid RT as a intensity-weighted mean of RTs