writeRScript: Prints an R-script to the screen which can be used for xcms...

In IPO: Automated Optimization of XCMS Data Processing parameters

Description

This function prints a script of the optimized findPeaks, retcor and grouping parameters to the screen.

Usage

writeRScript(peakPickingSettings, retCorGroupSettings, nSlaves = 0)

Arguments

peakPickingSettings	The optimized settings for xcms-methods findPeaks.centWave or findPeaks.matchedFilter
retCorGroupSettings	The optimized settings for xcms-methods for retcor.obiwarp and group.density
nSlaves	DEPRECATED

Details

This function prints a script out of the optimized findPeaks, retcor and grouping parameters to the screen.

The function message is used to print the script. For capuring the output capture.output(writeRScript(...), type = "message") might be used.

Value

none

Author(s)

Gunnar Libiseller, Thomas Riebenbauer ([e-mail])

Examples

#creating list of peak picking parameters
paramsPP <- list(min_peakwidth=5, max_peakwidth=12, ppm=58,
                  mzdiff=-0.001, snthresh=10, noise=0, prefilter=3, 
                  value_of_prefilter=100,  mzCenterFun="wMean", integrate=1, 
                  fitgauss=FALSE, verbose.columns=FALSE, nSlaves=1)
                  

#creating list of retention time correction and grouping parameters
paramsRTCGroup <- list(retcorMethod="obiwarp", distFunc="cor", gapInit=0.2, 
                       gapExtend=2.4, profStep=1, plottype="none", response=1,  
                       factorDiag=2, factorGap=1, localAlignment=0, initPenalty=0,
                       bw=30, minfrac=0.5, minsamp=1, mzwid=0.25, max=50)

#outputting an xcms-script to the display
writeRScript(paramsPP, paramsRTCGroup, 4)

IPO documentation built on Nov. 8, 2020, 8:31 p.m.