writeParamsTable: Writes XCMS settings to a file.

In IPO: Automated Optimization of XCMS Data Processing parameters

Description

This function writes findPeaks, retcor and grouping parameters to a file using write.table.

Usage

writeParamsTable(peakPickingSettings, retCorGroupSettings, file, ...)

Arguments

peakPickingSettings	A list of optimized settings for xcms-methods findPeaks.centWave or findPeaks.matchedFilter
retCorGroupSettings	A list of optimized settings for xcms-methods for retcor.obiwarp and group.density
file	The name of the outputfile for the parameters.
...	Additional parameters for write.table.

Details

This function writes findPeaks, retcor and grouping parameters to a file using write.table.

Value

none

Author(s)

Gunnar Libiseller

See Also

xcms

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)

#writing parameters to the file "params.tsv"
writeParamsTable(paramsPP, paramsRTCGroup, "params.tsv")

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