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FeatureFinderAlgorithmSimplest Parameters

Parameters of FeatureFinderAlgorithmSimplest:

NameTypeDefaultRestrictionsDescription
seeder:min_intensityfloat1min: 0Absolute value for the minimum intensity of a seed. If set to 0, a fixed percentage of the intensity of the largest peak is taken (see intensity_perc).
seeder:intensity_percfloat20min: 0 max: 100Minimum percentage of the intensity of the largest peak that a seed has to have (used only if min_intensity is set to 0).
extender:dist_mz_upfloat6min: 0Maximum high m/z distance of peak in the region/boundary from the seed.
extender:dist_mz_downfloat2min: 0Maximum low m/z distance of peak in the region/boundary from the seed.
extender:dist_rt_upfloat5min: 0Maximum high RT distance of peak in the region/boundary from the seed.
extender:dist_rt_downfloat5min: 0Maximum low RT distance of peak in the region/boundary from the seed.
extender:priority_thrfloat-0.1 Minimum priority for data points to be included into the boundary of the feature (default 0.0). The priority of a data point is a function of its intensity and its distance to the last point included into the feature region. Setting this threshold to zero or a very small value is usually a good idea.
extender:intensity_factorfloat0.03min: 0 max: 1Influences for intensity (ion count) threshold in the feature extension. We include only raw data points into this region if their intensity is larger than [intensity_factor * (intensity of the seed)].
fitter:fit_algorithmstringsimplesimple, simplest, waveletFitting algorithm type (internal parameter).
fitter:max_iterationint500min: 1Maximum number of iterations for fitting with Levenberg-Marquardt algorithm.
fitter:deltaAbsErrorfloat0.0001min: 0Absolute error used by the Levenberg-Marquardt algorithm.
fitter:deltaRelErrorfloat0.0001min: 0Relative error used by the Levenberg-Marquardt algorithm.
fitter:tolerance_stdev_bounding_boxfloat3min: 0Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data
fitter:intensity_cutoff_factorfloat0.05min: 0 max: 1Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model
fitter:feature_intensity_sumint1min: 0 max: 1Determines what is reported as feature intensity.
1: the sum of peak intensities;
0: the maximum intensity of all peaks
fitter:min_num_peaks:finalint5min: 1Minimum number of peaks left after cutoff. If smaller, feature will be discarded.
fitter:min_num_peaks:extendedint10min: 1Minimum number of peaks after extension. If smaller, feature will be discarded.
fitter:rt:interpolation_stepfloat0.2min: 0Step size in seconds used to interpolate model for RT.
fitter:mz:interpolation_stepfloat0.03min: 0.001Interpolation step size for m/z.
fitter:mz:model_type:firstint0min: 0Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian).
fitter:mz:model_type:lastint4min: 0Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian).
fitter:quality:typestringCorrelationCorrelationType of the quality measure used to assess the fit of model vs data.
fitter:quality:minimumfloat0.65min: 0 max: 1Minimum quality of fit, features below this threshold are discarded.
fitter:isotope_model:stdev:firstfloat0.04min: 0First standard deviation to be considered for isotope model.
fitter:isotope_model:stdev:lastfloat0.12min: 0Last standard deviation to be considered for isotope model.
fitter:isotope_model:stdev:stepfloat0.04min: 0Step size for standard deviations considered for isotope model.
fitter:isotope_model:averagines:Cfloat0.0443min: 0Number of C atoms per Dalton of the mass.
fitter:isotope_model:averagines:Hfloat0.007min: 0Number of H atoms per Dalton of the mass.
fitter:isotope_model:averagines:Nfloat0.0012min: 0Number of N atoms per Dalton of the mass.
fitter:isotope_model:averagines:Ofloat0.013min: 0Number of O atoms per Dalton of the mass.
fitter:isotope_model:averagines:Sfloat0.00037min: 0Number of S atoms per Dalton of the mass.
fitter:isotope_model:isotope:trim_right_cutofffloat0.001min: 0Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered.
fitter:isotope_model:isotope:maximumint100min: 1Maximum number of isotopes being used for the IsotopeModel.
fitter:isotope_model:isotope:distancefloat1.000495min: 0Distance between consecutive isotopic peaks.

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