Kernel_MassTrace#

class pyopenms.Kernel_MassTrace#

Bases: object

Cython implementation of _Kernel_MassTrace

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: Kernel_MassTrace) None

Overload:

__init__(self, trace_peaks: List[Peak2D]) None

Methods

__init__

Overload:

computeFwhmArea(self)

computeFwhmAreaSmooth(self)

Computes chromatographic peak area within the FWHM range.

computePeakArea(self)

Sums intensities of all peaks in the mass trace

computeSmoothedPeakArea(self)

Sums all non-negative (smoothed!) intensities in the mass trace

estimateFWHM(self, in_0)

Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)

findMaxByIntPeak(self, in_0)

Returns the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities)

getAverageMS1CycleTime(self)

Returns average scan time of mass trace

getCentroidMZ(self)

Returns the centroid m/z

getCentroidRT(self)

Returns the centroid RT

getCentroidSD(self)

Returns the centroid SD

getConvexhull(self)

Returns the mass trace's convex hull

getFWHM(self)

Returns FWHM

getFWHMborders(self)

Returns FWHM boarders

getIntensity(self, in_0)

Returns the intensity

getLabel(self)

Returns label of mass trace

getMaxIntensity(self, in_0)

Returns the max intensity

getQuantMethod(self)

Check if area or median is used for quantification

getSize(self)

Returns the number of peaks contained in the mass trace

getSmoothedIntensities(self)

Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)

getTraceLength(self)

Returns the length of the trace (as difference in RT)

setCentroidSD(self, tmp_sd)

setLabel(self, label)

Sets label of mass trace

setQuantMethod(self, method)

Determine if area or median is used for quantification

setSmoothedIntensities(self, db_vec)

Sets smoothed intensities (smoothing is done externally, e.g.

updateMeanMZ(self)

Compute & update centroid m/z as mean of m/z values

updateMedianMZ(self)

Compute & update centroid m/z as median of m/z values

updateMedianRT(self)

Compute & update centroid RT as median position of intensities

updateSmoothedMaxRT(self)

updateSmoothedWeightedMeanRT(self)

updateWeightedMZsd(self)

Compute & update m/z standard deviation of mass trace as weighted mean of m/z values

updateWeightedMeanMZ(self)

Compute & update centroid m/z as weighted mean of m/z values

updateWeightedMeanRT(self)

Compute & update centroid RT as a intensity-weighted mean of RTs

Attributes

computeFwhmArea(self) float#
computeFwhmAreaSmooth(self) float#

Computes chromatographic peak area within the FWHM range.

computePeakArea(self) float#

Sums intensities of all peaks in the mass trace

computeSmoothedPeakArea(self) float#

Sums all non-negative (smoothed!) intensities in the mass trace

estimateFWHM(self, in_0: bool) int#

Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)

findMaxByIntPeak(self, in_0: bool) int#

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(self) float#

Returns average scan time of mass trace

getCentroidMZ(self) float#

Returns the centroid m/z

getCentroidRT(self) float#

Returns the centroid RT

getCentroidSD(self) float#

Returns the centroid SD

getConvexhull(self) ConvexHull2D#

Returns the mass trace’s convex hull

getFWHM(self) float#

Returns FWHM

getFWHMborders(self) List[int, int]#

Returns FWHM boarders

getIntensity(self, in_0: bool) float#

Returns the intensity

getLabel(self) bytes | str | String#

Returns label of mass trace

getMaxIntensity(self, in_0: bool) float#

Returns the max intensity

getQuantMethod(self) int#

Check if area or median is used for quantification

getSize(self) int#

Returns the number of peaks contained in the mass trace

getSmoothedIntensities(self) List[float]#

Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)

getTraceLength(self) float#

Returns the length of the trace (as difference in RT)

setCentroidSD(self, tmp_sd: float) None#
setLabel(self, label: bytes | str | String) None#

Sets label of mass trace

setQuantMethod(self, method: int) None#

Determine if area or median is used for quantification

setSmoothedIntensities(self, db_vec: List[float]) None#

Sets smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing)

updateMeanMZ(self) None#

Compute & update centroid m/z as mean of m/z values

updateMedianMZ(self) None#

Compute & update centroid m/z as median of m/z values

updateMedianRT(self) None#

Compute & update centroid RT as median position of intensities

updateSmoothedMaxRT(self) None#
updateSmoothedWeightedMeanRT(self) None#
updateWeightedMZsd(self) None#

Compute & update m/z standard deviation of mass trace as weighted mean of m/z values

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

updateWeightedMeanMZ(self) None#

Compute & update centroid m/z as weighted mean of m/z values

updateWeightedMeanRT(self) None#

Compute & update centroid RT as a intensity-weighted mean of RTs