combineParams: Combining two lists of parameters together.
In IPO: Automated Optimization of XCMS Data Processing parameters

Description Usage Arguments Details Value Author(s) Examples

This function combines two lists of parameters. The first is a list of parameters which should be optimized. These parameters have different values set by Design of Experimnt. The second list consists of parameters which should not be optimized, hence only one value is set for each parameter. The parameters of the second list are replicated to have the same length as the number experiments in the DoE. Then the two lists are combined.

1	combineParams(params_1, params_2)

`params_1`	A list holding parameters which should be optimized. Each parameter already has value set for each experiment of an Design of Experiment.
`params_2`	A list holding parameters which should not be optimized, hence only one value is set.

Special treatment is needed for the findPeaks.matchedFilter-parameters 'sigma', 'mzdiff' since these two parameters are defined by default relative to the parameters 'fwhm' or 'step' and 'steps' respectively.
sigma=fwhm/2.3548 mzdiff=0.8-step*steps

A list of consting of all parameters needed for an xcms-method (findPeaks.centWave, findPeaks.matchedFilter, retcor.obiwarp or group.density). Each list item has the same length which is equal to the number of experiments within the DoE.

Gunnar Libiseller

params <- getDefaultXcmsSetStartingParams()
typ_params <- typeCastParams(params)
design <- getBbdParameter(typ_params$to_optimize) 
xcms_design <- decode.data(design) 
xcms_design <- combineParams(xcms_design, typ_params$no_optimization)  
xcms_design