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
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)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
- 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 #
- 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