Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
fit_algorithm | string | simple | simple, simplest, wavelet | Fitting algorithm type (internal parameter). |
max_iteration | int | 500 | min: 1 | Maximum number of iterations for fitting with Levenberg-Marquardt algorithm. |
deltaAbsError | float | 0.0001 | min: 0 | Absolute error used by the Levenberg-Marquardt algorithm. |
deltaRelError | float | 0.0001 | min: 0 | Relative error used by the Levenberg-Marquardt algorithm. |
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 |
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 |
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 |
min_num_peaks:final | int | 5 | min: 1 | Minimum number of peaks left after cutoff. If smaller, feature will be discarded. |
min_num_peaks:extended | int | 10 | min: 1 | Minimum number of peaks after extension. If smaller, feature will be discarded. |
rt:interpolation_step | float | 0.2 | min: 0 | Step size in seconds used to interpolate model for RT. |
mz:interpolation_step | float | 0.03 | min: 0.001 | Interpolation step size for m/z. |
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). |
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). |
quality:type | string | Correlation | Correlation | Type of the quality measure used to assess the fit of model vs data. |
quality:minimum | float | 0.65 | min: 0 max: 1 | Minimum quality of fit, features below this threshold are discarded. |
isotope_model:stdev:first | float | 0.04 | min: 0 | First standard deviation to be considered for isotope model. |
isotope_model:stdev:last | float | 0.12 | min: 0 | Last standard deviation to be considered for isotope model. |
isotope_model:stdev:step | float | 0.04 | min: 0 | Step size for standard deviations considered for isotope model. |
isotope_model:averagines:C | float | 0.0443 | min: 0 | Number of C atoms per Dalton of the mass. |
isotope_model:averagines:H | float | 0.007 | min: 0 | Number of H atoms per Dalton of the mass. |
isotope_model:averagines:N | float | 0.0012 | min: 0 | Number of N atoms per Dalton of the mass. |
isotope_model:averagines:O | float | 0.013 | min: 0 | Number of O atoms per Dalton of the mass. |
isotope_model:averagines:S | float | 0.00037 | min: 0 | Number of S atoms per Dalton of the mass. |
isotope_model:isotope:trim_right_cutoff | float | 0.001 | min: 0 | Cutoff for averagine distribution, trailing isotopes below this relative intensity are not considered. |
isotope_model:isotope:maximum | int | 100 | min: 1 | Maximum number of isotopes being used for the IsotopeModel. |
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 |