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MapRTTransformer

Applies retention time transformations to maps.

potential predecessor tools $ \longrightarrow $ MapRTTransformer $ \longrightarrow $ 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.

See Also
MapAlignerIdentification MapAlignerPoseClustering MapAlignerSpectrum

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):
NameTypeDefaultRestrictionsDescription
type stringnone none, linear, b_spline, interpolatedType of model
linear:symmetric_regression stringfalse true, falsePerform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.
b_spline:wavelength float0 min: 0Determines 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 int5 min: 0Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing.
b_spline:extrapolate stringlinear linear, b_spline, constant, global_linearMethod 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 int2 min: 0 max: 2Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)
interpolated:interpolation_type stringcspline linear, cspline, akimaType of interpolation to apply.

Note
As output options, either 'out' or 'trafo_out' has to be provided. They can be used together.
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

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:

Legend:
required parameter
advanced parameter
+MapRTTransformerApplies retention time transformations to maps.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MapRTTransformer'
in[] Input files to transform (separated by blanks)input file*.mzML,*.featureXML,*.consensusXML,*.idXML
out[] Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together.output file*.mzML,*.featureXML,*.consensusXML,*.idXML
trafo_in[] Transformations to apply (files separated by blanks)input file*.trafoXML
trafo_out[] Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together.output file*.trafoXML
invertfalse Invert transformations (approximatively) before applying themtrue,false
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false
+++modelOptions to control the modeling of retention time transformations from data
typenone Type of modelnone,linear,b_spline,interpolated
++++linearParameters for 'linear' model
symmetric_regressionfalse Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.true,false
++++b_splineParameters for 'b_spline' model
wavelength0 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.0:∞
num_nodes5 Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing.0:∞
extrapolatelinear 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).linear,b_spline,constant,global_linear
boundary_condition2 Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)0:2
++++interpolatedParameters for 'interpolated' model
interpolation_typecspline Type of interpolation to apply.linear,cspline,akima

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:43 using doxygen 1.8.5