addIdentInfo	addIdentInfo
addIdentInfo,metaXpara,character-method	addIdentInfo
addValueNorm<-	addValueNorm
addValueNorm<-,metaXpara,metaXpara-method	metaXpara-class
autoRemoveOutlier	autoRemoveOutlier
autoRemoveOutlier,metaXpara-method	autoRemoveOutlier
bootPLSDA	bootPLSDA
calcAUROC	calcAUROC
calcAUROC,numeric-method	calcAUROC
calcVIP	calcVIP
calcVIP,ANY-method	calcVIP
center<-	center
center<-,plsDAPara-method	plsDAPara-class
cor.network	cor.network
createModels	createModels
dataClean	dataClean
dataClean,metaXpara-method	dataClean
dir.case<-	dir.case
dir.case<-,metaXpara-method	metaXpara-class
dir.ctrl<-	dir.ctrl
dir.ctrl<-,metaXpara-method	metaXpara-class
doQCRLSC	doQCRLSC
doQCRLSC,metaXpara-method	doQCRLSC
featureSelection	featureSelection
filterPeaks	filterPeaks
filterPeaks,metaXpara-method	filterPeaks
filterQCPeaks	filterQCPeaks
filterQCPeaks,metaXpara-method	filterQCPeaks
filterQCPeaksByCV	filterQCPeaksByCV
filterQCPeaksByCV,metaXpara-method	filterQCPeaksByCV
getPeaksTable	getPeaksTable
getPeaksTable,metaXpara-method	getPeaksTable
group.bw0<-	group.bw0
group.bw0<-,metaXpara-method	metaXpara-class
group.bw<-	group.bw
group.bw<-,metaXpara-method	metaXpara-class
group.max<-	group.max
group.max<-,metaXpara-method	metaXpara-class
group.minfrac<-	group.minfrac
group.minfrac<-,metaXpara-method	metaXpara-class
group.minsamp<-	group.minsamp
group.minsamp<-,metaXpara-method	metaXpara-class
group.mzwid0<-	group.mzwid0
group.mzwid0<-,metaXpara-method	metaXpara-class
group.mzwid<-	group.mzwid
group.mzwid<-,metaXpara-method	metaXpara-class
group.sleep<-	group.sleep
group.sleep<-,metaXpara-method	metaXpara-class
hasQC	hasQC
hasQC,metaXpara-method	hasQC
idres<-	idres
idres<-,metaXpara-method	metaXpara-class
kfold<-	kfold
kfold<-,plsDAPara-method	plsDAPara-class
makeDirectory	makeDirectory
makeDirectory,metaXpara-method	makeDirectory
makeMetaboAnalystInput	makeMetaboAnalystInput
makeMetaboAnalystInput,metaXpara-method	makeMetaboAnalystInput
metaboliteAnnotation	metaboliteAnnotation
metaXpara-class	metaXpara-class
metaXpipe	metaXpipe
metaXpipe,metaXpara-method	metaXpipe
method<-	method
method<-,plsDAPara-method	plsDAPara-class
missingValueImpute	missingValueImpute
missingValueImpute,data.frame-method	missingValueImpute
missingValueImpute,metaXpara-method	missingValueImpute
missValueImputeMethod<-	missValueImputeMethod
missValueImputeMethod<-,metaXpara-method	metaXpara-class
myCalcAUROC	myCalcAUROC
myPLSDA	myPLSDA
myPLSDA,ANY,ANY,ANY,ANY-method	myPLSDA
myPLSDA,ANY,ANY,logical,ANY-method	myPLSDA
myPLSDA,ANY,ANY,missing,logical-method	myPLSDA
ncomp<-	ncomp
ncomp<-,plsDAPara-method	plsDAPara-class
normalize	normalize
normalize,metaXpara-method	normalize
nperm<-	nperm
nperm<-,plsDAPara-method	plsDAPara-class
outdir<-	outdir
outdir<-,metaXpara-method	metaXpara-class
pathwayAnalysis	pathwayAnalysis
peakFinder	peakFinder
peakFinder,metaXpara-method	peakFinder
peaksData<-	peaksData
peaksData<-,metaXpara-method	metaXpara-class
peakStat	peakStat
peakStat,metaXpara,plsDAPara-method	peakStat
permutePLSDA	permutePLSDA
plotCorHeatmap	plotCorHeatmap
plotCV	plotCV
plotCV,metaXpara-method	plotCV
plotHeatMap	plotHeatMap
plotHeatMap,metaXpara-method	plotHeatMap
plotIntDistr	plotIntDistr
plotIntDistr,metaXpara-method	plotIntDistr
plotMissValue	plotMissValue
plotMissValue,metaXpara-method	plotMissValue
plotNetwork	plotNetwork
plotPCA	plotPCA
plotPCA,metaXpara-method	plotPCA
plotPeakBox	plotPeakBox
plotPeakBox,metaXpara-method	plotPeakBox
plotPeakNumber	plotPeakNumber
plotPeakNumber,metaXpara-method	plotPeakNumber
plotPeakSN	plotPeakSN
plotPeakSN,metaXpara-method	plotPeakSN
plotPeakSumDist	plotPeakSumDist
plotPeakSumDist,metaXpara-method	plotPeakSumDist
plotPLSDA	plotPLSDA
plotPLSDA,metaXpara-method	plotPLSDA
plotQC	plotQC
plotQC,metaXpara-method	plotQC
plotQCRLSC	plotQCRLSC
plotQCRLSC,metaXpara-method	plotQCRLSC
plotTreeMap	plotTreeMap
plotTreeMap,metaXpara-method	plotTreeMap
plsDAPara-class	plsDAPara-class
powerAnalyst	powerAnalyst
prefix<-	prefix
prefix<-,metaXpara-method	metaXpara-class
preProcess	preProcess
qcRlscSpan<-	qcRlscSpan
qcRlscSpan<-,metaXpara-method	metaXpara-class
ratioPairs<-	ratioPairs
ratioPairs<-,metaXpara-method	metaXpara-class
rawPeaks<-	rawPeaks
rawPeaks<-,metaXpara-method	metaXpara-class
removeSample	removeSample
removeSample,metaXpara-method	removeSample
reSetPeaksData	reSetPeaksData
reSetPeaksData,metaXpara-method	reSetPeaksData
retcor.method<-	retcor.method
retcor.method<-,metaXpara-method	metaXpara-class
retcor.plottype<-	retcor.plottype
retcor.plottype<-,metaXpara-method	metaXpara-class
retcor.profStep<-	retcor.profStep
retcor.profStep<-,metaXpara-method	metaXpara-class
runPLSDA	runPLSDA
sampleListFile<-	sampleListFile
sampleListFile<-,metaXpara-method	metaXpara-class
scale<-	scale
scale<-,plsDAPara-method	plsDAPara-class
selectBestComponent	selectBestComponent
t<-	t
t<-,plsDAPara-method	plsDAPara-class
transformation	transformation
validation<-	validation
validation<-,plsDAPara-method	plsDAPara-class
xcmsSet.fitgauss<-	xcmsSet.fitgauss
xcmsSet.fitgauss<-,metaXpara-method	metaXpara-class
xcmsSet.fwhm<-	xcmsSet.fwhm
xcmsSet.fwhm<-,metaXpara-method	metaXpara-class
xcmsSet.integrate<-	xcmsSet.integrate
xcmsSet.integrate<-,metaXpara-method	metaXpara-class
xcmsSet.max<-	xcmsSet.max
xcmsSet.max<-,metaXpara-method	metaXpara-class
xcmsSet.method<-	xcmsSet.method
xcmsSet.method<-,metaXpara-method	metaXpara-class
xcmsSet.mzCenterFun<-	xcmsSet.mzCenterFun
xcmsSet.mzCenterFun<-,metaXpara-method	metaXpara-class
xcmsSet.mzdiff<-	xcmsSet.mzdiff
xcmsSet.mzdiff<-,metaXpara-method	metaXpara-class
xcmsSet.noise<-	xcmsSet.noise
xcmsSet.noise<-,metaXpara-method	metaXpara-class
xcmsSet.nSlaves<-	xcmsSet.nSlaves
xcmsSet.nSlaves<-,metaXpara-method	metaXpara-class
xcmsSet.peakwidth<-	xcmsSet.peakwidth
xcmsSet.peakwidth<-,metaXpara-method	metaXpara-class
xcmsSet.polarity<-	xcmsSet.polarity
xcmsSet.polarity<-,metaXpara-method	metaXpara-class
xcmsSet.ppm<-	xcmsSet.ppm
xcmsSet.ppm<-,metaXpara-method	metaXpara-class
xcmsSet.prefilter<-	xcmsSet.prefilter
xcmsSet.prefilter<-,metaXpara-method	metaXpara-class
xcmsSet.profparam<-	xcmsSet.profparam
xcmsSet.profparam<-,metaXpara-method	metaXpara-class
xcmsSet.sleep<-	xcmsSet.sleep
xcmsSet.sleep<-,metaXpara-method	metaXpara-class
xcmsSet.snthresh<-	xcmsSet.snthresh
xcmsSet.snthresh<-,metaXpara-method	metaXpara-class
xcmsSet.step<-	xcmsSet.step
xcmsSet.step<-,metaXpara-method	metaXpara-class
xcmsSet.verbose.columns<-	xcmsSet.verbose.columns
xcmsSet.verbose.columns<-,metaXpara-method	metaXpara-class
xcmsSetObj<-	xcmsSetObj
xcmsSetObj<-,metaXpara-method	metaXpara-class
zero2NA	zero2NA
zero2NA,metaXpara-method	zero2NA
