optimizeRetGroup: Optimization for parameters for retention time correction and...
In IPO: Automated Optimization of XCMS Data Processing parameters

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/optimizeRetCorGroupParameters.R

This function provides optimisation for parameters of the xcms-method retcor.obiwarp and group.density. The retention time correction is optimised by minimizing intra-feature retention time shifts; grouping is optimized by increasing the number of features which have exactly one peak per sample.

1 2	optimizeRetGroup(xset, params = getDefaultRetGroupStartingParams(), nSlaves = 4, subdir = "IPO", plot = TRUE)

`xset`	`xcmsSet` object
`params`	A list of parameters which are needed by xcms-methods retcor.obiwarp and group.density. List-items with two values will be optimized. The first value defines the lower test value, the second one the higher test value.
`nSlaves`	Number of slaves the optimization process should spawn.
`subdir`	The name of the subdirectory which is created and where the figures of the response surface models will be saved to. `NULL` plots the figures to the graphic device. This parameter is ignored, if `plot = TRUE`.
`plot`	Defines if plots should be generated (`TRUE`) or not (`FALSE`). This parameter overwrites the `subdir`-parameter. Defaults to `TRUE`.

A LIST of length n+1 with n beeing the optimization runs needed

comp1-comp(n)

A LIST containing:
1. Parameters used for the nth optimization run
2. Box-Behnken or Central Composite Design used for optimization run
3. Responses from calculateRGTV for every experiment in the design
4. Response surface model for the design
5. The normalized parameter settings giving the best Retention time and Grouping Target Value (RGTV) (values between -1 and 1) 6. Response from calculateRGTV for xcmsSet-object created with best parameters in this run 7. xcmsSet-object created with best parameters in this run

comp(n+1)

A LIST containing:
1. Parameters giving the best RGTV

Gunnar Libiseller

Obiwarp Prince, J. T., & Marcotte, E. M. (2006). Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Analytical chemistry, 78(17), 6140-52. doi:10.1021/ac0605344

getDefaultRetGroupStartingParams

 

mtbls2files <- list.files(file.path(find.package("mtbls2"), "mzData"), 
                          full.names=TRUE)

params <- list(min_peakwidth=12, max_peakwidth=30, ppm=30,
                  mzdiff=-0.001, snthresh=10, noise=10000, prefilter=3, 
                  value_of_prefilter=100,  mzCenterFun="wMean", integrate=1, 
                  fitgauss=FALSE, verbose.columns=FALSE, nSlaves=2)

xset <- calculateXcmsSet(mtbls2files[1:2], params)


#optimize the retention time correction and grouping parameters
paramsRG <- getDefaultRetGroupStartingParams()
paramsRG$profStep <- 1
paramsRG$minfrac <- 0.75
resultRG <- optimizeRetGroup(xset, params=paramsRG, 
                             nSlaves=4,subdir="mtbls2")

writeRScript(params, resultRG$best_settings, 4)