Applies retention time transformations to maps.
potential predecessor tools | ![]() ![]() | potential successor tools |
MapAlignerIdentification (or another alignment algorithm) | FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT |
This tool can apply retention time transformations to different types of data (mzML, featureXML, consensusXML, and idXML files). The transformations might have been generated by a previous invocation of one of the MapAligner tools (linked below). However, the trafoXML file format is not very complicated, so it is relatively easy to write (or generate) your own files. Each input file will give rise to one output file.
With this tool it is also possible to invert transformations, or to fit a different model than originally specified to the retention time data in the transformation files. To fit a new model, choose a value other than "none" for the model type (see below).
Since OpenMS 1.8, the extraction of data for the alignment has been separate from the modeling of RT transformations based on that data. It is now possible to use different models independently of the chosen algorithm. The different available models are:
The following parameters control the modeling of RT transformations (they can be set in the "model" section of the INI file):
Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
type | string | none | none, linear, b_spline, interpolated | Type of model |
linear:symmetric_regression | string | false | true, false | Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'. |
b_spline:wavelength | float | 0 | min: 0 | Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points. |
b_spline:num_nodes | int | 5 | min: 0 | Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing. |
b_spline:extrapolate | string | linear | linear, b_spline, constant, global_linear | Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range). |
b_spline:boundary_condition | int | 2 | min: 0 max: 2 | Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero) |
interpolated:interpolation_type | string | cspline | linear, cspline, akima | Type of interpolation to apply. |
The command line parameters of this tool are:
MapRTTransformer -- Applies retention time transformations to maps. Version: 2.0.0 Mar 30 2016, 12:52:33, Revision: GIT-NOTFOUND Usage: MapRTTransformer <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the --helphelp option. Options (mandatory options marked with '*'): -in <files> Input files to transform (separated by blanks) (valid formats: 'mzML', 'featureXML', 'consensusXML', 'idXML') -out <files> Output files separated by blanks. Either this option or 'trafo_out' have to be provided . They can be used together. (valid formats: 'mzML', 'featureXML', 'consensusXML', 'idX ML') -trafo_in <files>* Transformations to apply (files separated by blanks) (valid formats: 'trafoXML') -trafo_out <files> Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together. (valid formats: 'trafoXML') -invert Invert transformations (approximatively) before applying them Common TOPP options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced) The following configuration subsections are valid: - model Options to control the modeling of retention time transformations from data You can write an example INI file using the '-write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5 |