MapRTTransformer

Applies retention time transformations to maps.

potential predecessor tools	$\longrightarrow$ MapRTTransformer $\longrightarrow$	potential successor tools
MapAlignerIdentification (or another alignment algorithm)	$\longrightarrow$ MapRTTransformer $\longrightarrow$	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).

Original retention time values can be kept as meta data. With the option store_original_rt, meta values with the name "original_RT" and the original retention time will be created for every major data element (spectrum, chromatogram, feature, consensus feature, peptide identification), unless they already exist - "original_RT" values from a previous invocation will not be overwritten.

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:

linear: Linear model.
b_spline: Smoothing spline (non-linear).
interpolated: Different types of interpolation.

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, lowess, 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)

lowess:span float 0.666666666666667 min: 0 max: 1 Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.

lowess:num_iterations int 3 min: 0 Number of robustifying iterations for lowess fitting.

lowess:delta float -1 Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.

lowess:interpolation_type string cspline linear, cspline, akima Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation

lowess:extrapolation_type string four-point-linear two-point-linear, four-point-linear, global-linear Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.

interpolated:interpolation_type string cspline linear, cspline, akima Type of interpolation to apply.

interpolated:extrapolation_type string two-point-linear two-point-linear, four-point-linear, global-linear Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.

Name	Type	Default	Restrictions	Description
type	string	none	none, linear, b_spline, lowess, 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)
lowess:span	float	0.666666666666667	min: 0 max: 1	Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.
lowess:num_iterations	int	3	min: 0	Number of robustifying iterations for lowess fitting.
lowess:delta	float	-1		Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.
lowess:interpolation_type	string	cspline	linear, cspline, akima	Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation
lowess:extrapolation_type	string	four-point-linear	two-point-linear, four-point-linear, global-linear	Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.
interpolated:interpolation_type	string	cspline	linear, cspline, akima	Type of interpolation to apply.
interpolated:extrapolation_type	string	two-point-linear	two-point-linear, four-point-linear, global-linear	Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.

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: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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 <file>           Input file to transform (separated by blanks) (valid formats: 'mzML', 'featureXML', 
                       'consensusXML', 'idXML')
  -out <file>          Output file (same file type as 'in'). Either this option or 'trafo_out' has to be prov
                       ided; they can be used together. (valid formats: 'mzML', 'featureXML', 'consensusXML',
                       'idXML')
  -trafo_in <file>*    Transformation to apply (valid formats: 'trafoXML')
  -trafo_out <file>    Transformation output file. Either this option or 'out' has to be provided; they can 
                       be used together. (valid formats: 'trafoXML')
  -invert              Invert transformation (approximatively) before applying it
  -store_original_rt   Store the original retention times (before transformation) as meta data in the output 
                       file
                       
                       
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.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MapRTTransformer'

in Input file to transform (separated by blanks)input file*.mzML,*.featureXML,*.consensusXML,*.idXML

out Output file (same file type as 'in'). Either this option or 'trafo_out' has to be provided; they can be used together.output file*.mzML,*.featureXML,*.consensusXML,*.idXML

trafo_in Transformation to applyinput file*.trafoXML

trafo_out Transformation output file. Either this option or 'out' has to be provided; they can be used together.output file*.trafoXML

invertfalse Invert transformation (approximatively) before applying ittrue,false

store_original_rtfalse Store the original retention times (before transformation) as meta data in the output filetrue,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,lowess,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

++++lowessParameters for 'lowess' model

span0.666666666666667 Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.0:1

num_iterations3 Number of robustifying iterations for lowess fitting.0:∞

delta-1 Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.

interpolation_typecspline Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolationlinear,cspline,akima

extrapolation_typefour-point-linear Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.two-point-linear,four-point-linear,global-linear

++++interpolatedParameters for 'interpolated' model

interpolation_typecspline Type of interpolation to apply.linear,cspline,akima

extrapolation_typetwo-point-linear Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.two-point-linear,four-point-linear,global-linear