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:num_breakpoints | int | 5 | min: 2 | Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape. |
b_spline:break_positions | string | uniform | uniform, quantiles | How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval. |
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: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: MapRTTransformer <options> This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti on 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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |