IsotopeWaveletTransform
- class pyopenms.IsotopeWaveletTransform
Bases:
objectCython implementation of _IsotopeWaveletTransform[_Peak1D]
Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1IsotopeWaveletTransform[_Peak1D].html
- __init__()
Cython signature: void IsotopeWaveletTransform(double min_mz, double max_mz, unsigned int max_charge, size_t max_scan_size, bool hr_data, String intenstype)
Cython signature: void IsotopeWaveletTransform(IsotopeWaveletTransform &)
Methods
Cython signature: void IsotopeWaveletTransform(double min_mz, double max_mz, unsigned int max_charge, size_t max_scan_size, bool hr_data, String intenstype)
Cython signature: void computeMinSpacing(MSSpectrum & c_ref)
Cython signature: double getLinearInterpolation(double mz_a, double intens_a, double mz_pos, double mz_b, double intens_b)
Cython signature: size_t getMaxScanSize()
Cython signature: double getMinSpacing()
Cython signature: double getSigma()
Cython signature: void getTransform(MSSpectrum & c_trans, MSSpectrum & c_ref, unsigned int c)
Cython signature: void getTransformHighRes(MSSpectrum & c_trans, MSSpectrum & c_ref, unsigned int c)
Cython signature: void identifyCharge(MSSpectrum & candidates, MSSpectrum & ref, unsigned int scan_index, unsigned int c, double ampl_cutoff, bool check_PPMs)
Cython signature: void initializeScan(MSSpectrum & c_ref, unsigned int c)
Cython signature: FeatureMap mapSeeds2Features(MSExperiment & map_, unsigned int RT_votes_cutoff)
Cython signature: void setSigma(double sigma)
Cython signature: void updateBoxStates(MSExperiment & map_, size_t scan_index, unsigned int RT_interleave, unsigned int RT_votes_cutoff, int front_bound, int end_bound)
- computeMinSpacing()
Cython signature: void computeMinSpacing(MSSpectrum & c_ref)
- getLinearInterpolation()
Cython signature: double getLinearInterpolation(double mz_a, double intens_a, double mz_pos, double mz_b, double intens_b)
- Parameters
mz_a – The m/z value of the point left to the query
intens_a – The intensity value of the point left to the query
mz_pos – The query point
mz_b – The m/z value of the point right to the query
intens_b – The intensity value of the point left to the query
- getMaxScanSize()
Cython signature: size_t getMaxScanSize()
- getMinSpacing()
Cython signature: double getMinSpacing()
- getSigma()
Cython signature: double getSigma()
- getTransform()
Cython signature: void getTransform(MSSpectrum & c_trans, MSSpectrum & c_ref, unsigned int c)
- Parameters
c_trans – The transform
c_ref – The reference spectrum
c – The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform
- getTransformHighRes()
Cython signature: void getTransformHighRes(MSSpectrum & c_trans, MSSpectrum & c_ref, unsigned int c)
- Parameters
c_trans – The transform
c_ref – The reference spectrum
c – The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform
- identifyCharge()
Cython signature: void identifyCharge(MSSpectrum & candidates, MSSpectrum & ref, unsigned int scan_index, unsigned int c, double ampl_cutoff, bool check_PPMs)
Given an isotope wavelet transformed spectrum ‘candidates’, this function assigns to every significant pattern its corresponding charge state and a score indicating the reliability of the prediction. The result of this process is stored internally. Important: Before calling this function, apply updateRanges() to the original map —– :param candidates: A isotope wavelet transformed spectrum. Entry “number i” in this vector must correspond to the charge-“(i-1)”-transform of its mass signal. (This is exactly the output of the function getTransforms.) :param ref: The reference scan (the untransformed raw data) corresponding to candidates :param c: The corresponding charge state minus 1 (e.g. c=2 means charge state 3) :param scan_index: The index of the scan (w.r.t. to some map) currently under consideration :param ampl_cutoff: The thresholding parameter. This parameter is the only (and hence a really important) parameter of the isotope wavelet transform. On the basis of ampl_cutoff the program tries to distinguish between noise and signal. Please note that it is not a “simple” hard thresholding parameter in the sense of drawing a virtual line in the spectrum, which is then used as a guillotine cut. Maybe you should play around a bit with this parameter to get a feeling about its range. For peptide mass fingerprints on small data sets (like single MALDI-scans e.g.), it makes sense to start ampl_cutoff=0 or even ampl_cutoff=-1, indicating no thresholding at all. Note that also ampl_cutoff=0 triggers (a moderate) thresholding based on the average intensity in the wavelet transform :param check_PPMs: If enabled, the algorithm will check each monoisotopic mass candidate for its plausibility by computing the ppm difference between this mass and the averagine model
- initializeScan()
Cython signature: void initializeScan(MSSpectrum & c_ref, unsigned int c)
- mapSeeds2Features()
Cython signature: FeatureMap mapSeeds2Features(MSExperiment & map_, unsigned int RT_votes_cutoff)
- Parameters
map – The original map containing the data set to be analyzed
max_charge – The maximal charge state under consideration
RT_votes_cutoff – See the IsotopeWaveletFF class
- setSigma()
Cython signature: void setSigma(double sigma)
- updateBoxStates()
Cython signature: void updateBoxStates(MSExperiment & map_, size_t scan_index, unsigned int RT_interleave, unsigned int RT_votes_cutoff, int front_bound, int end_bound)
A function keeping track of currently open and closed sweep line boxes This function is used by the isotope wavelet feature finder and must be called for each processed scan —– :param map: The original map containing the data set to be analyzed :param scan_index: The index of the scan currently under consideration w.r.t. its MS map This information is necessary to sweep across the map after each scan has been evaluated :param RT_votes_cutoff: See the IsotopeWaveletFF class