Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
seeder:min_intensity | float | 1 | min: 0 | Absolute 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_perc | float | 20 | min: 0 max: 100 | Minimum 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_up | float | 6 | min: 0 | Maximum high m/z distance of peak in the region/boundary from the seed. |
extender:dist_mz_down | float | 2 | min: 0 | Maximum low m/z distance of peak in the region/boundary from the seed. |
extender:dist_rt_up | float | 5 | min: 0 | Maximum high RT distance of peak in the region/boundary from the seed. |
extender:dist_rt_down | float | 5 | min: 0 | Maximum low RT distance of peak in the region/boundary from the seed. |
extender:priority_thr | float | -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_factor | float | 0.03 | min: 0 max: 1 | Influences 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_algorithm | string | simple | simple, simplest, wavelet | Fitting algorithm type (internal parameter). |
fitter:max_iteration | int | 500 | min: 1 | Maximum number of iterations for fitting with Levenberg-Marquardt algorithm. |
fitter:deltaAbsError | float | 0.0001 | min: 0 | Absolute error used by the Levenberg-Marquardt algorithm. |
fitter:deltaRelError | float | 0.0001 | min: 0 | Relative error used by the Levenberg-Marquardt algorithm. |
fitter:tolerance_stdev_bounding_box | float | 3 | min: 0 | Bounding 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_factor | float | 0.05 | min: 0 max: 1 | Cutoff peaks with a predicted intensity below intensity_cutoff_factor times the maximal intensity of the model |
fitter:feature_intensity_sum | int | 1 | min: 0 max: 1 | Determines what is reported as feature intensity. 1: the sum of peak intensities; 0: the maximum intensity of all peaks |
fitter:min_num_peaks:final | int | 5 | min: 1 | Minimum number of peaks left after cutoff. If smaller, feature will be discarded. |
fitter:min_num_peaks:extended | int | 10 | min: 1 | Minimum number of peaks after extension. If smaller, feature will be discarded. |
fitter:rt:interpolation_step | float | 0.2 | min: 0 | Step size in seconds used to interpolate model for RT. |
fitter:mz:interpolation_step | float | 0.03 | min: 0.001 | Interpolation step size for m/z. |
fitter:mz:model_type:first | int | 0 | min: 0 | Numeric id of first m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian). |
fitter:mz:model_type:last | int | 4 | min: 0 | Numeric id of last m/z model fitted (usually indicating the charge state), 0 = no isotope pattern (fit a single gaussian). |
fitter:quality:type | string | Correlation | Correlation | Type of the quality measure used to assess the fit of model vs data. |
fitter:quality:minimum | float | 0.65 | min: 0 max: 1 | Minimum quality of fit, features below this threshold are discarded. |
fitter:isotope_model:stdev:first | float | 0.04 | min: 0 | First standard deviation to be considered for isotope model. |
fitter:isotope_model:stdev:last | float | 0.12 | min: 0 | Last standard deviation to be considered for isotope model. |
fitter:isotope_model:stdev:step | float | 0.04 | min: 0 | Step size for standard deviations considered for isotope model. |
fitter:isotope_model:averagines:C | float | 0.0443 | min: 0 | Number of C atoms per Dalton of the mass. |
fitter:isotope_model:averagines:H | float | 0.007 | min: 0 | Number of H atoms per Dalton of the mass. |
fitter:isotope_model:averagines:N | float | 0.0012 | min: 0 | Number of N atoms per Dalton of the mass. |
fitter:isotope_model:averagines:O | float | 0.013 | min: 0 | Number of O atoms per Dalton of the mass. |
fitter:isotope_model:averagines:S | float | 0.00037 | min: 0 | Number of S atoms per Dalton of the mass. |
fitter:isotope_model:isotope:trim_right_cutoff | float | 0.001 | min: 0 | Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered. |
fitter:isotope_model:isotope:maximum | int | 100 | min: 1 | Maximum number of isotopes being used for the IsotopeModel. |
fitter:isotope_model:isotope:distance | float | 1.000495 | min: 0 | Distance between consecutive isotopic peaks. |
Note:
Generated Tue Apr 1 15:36:40 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |