absent	absent-methods
absent,xcmsSet-method	absent-methods
AutoLockMass	AutoLockMass-methods
AutoLockMass,xcmsRaw-method	AutoLockMass-methods
AutoLockMass-methods	AutoLockMass-methods
c, c-methods	c.xcmsSet
c.xcmsSet	c.xcmsSet
calibrate	calibrate
calibrate,xcmsSet-method	calibrate
collect	collect-methods
collect,xcmsFragments-method	collect-methods
collect,xcmsRaw-method	collect-methods
collect-methods	collect-methods
colMax	colMax
deepCopy	xcmsRaw
deepCopy,xcmsRaw-method	xcmsRaw
descendMin	descendZero
descendValue	descendZero
descendZero	descendZero
diffreport	diffreport-methods
diffreport,xcmsSet-method	diffreport-methods
doubleMatrix	doubleMatrix
etg	etg
filepaths	xcmsSet-class
filepaths,xcmsSet-method	xcmsSet-class
filepaths<-	xcmsSet-class
filepaths<-,xcmsSet-method	xcmsSet-class
fillPeaks	fillPeaks-methods
fillPeaks,xcmsSet-method	fillPeaks-methods
fillPeaks.chrom	fillPeaks.chrom-methods
fillPeaks.chrom,xcmsSet-method	fillPeaks.chrom-methods
fillPeaks.MSW	fillPeaks.MSW-methods
fillPeaks.MSW,xcmsSet-method	fillPeaks.MSW-methods
filtfft	filtfft
findEqualGreater	findEqualGreater
findEqualGreaterM	findEqualGreater
findEqualLess	findEqualGreater
findMZ	findMZ
findMZ,xcmsFragments-method	findMZ
findneutral	findneutral
findneutral,xcmsFragments-method	findneutral
findPeaks	findPeaks-methods
findPeaks,xcmsRaw-method	findPeaks-methods
findPeaks-methods	findPeaks-methods
findPeaks.centWave	findPeaks.centWave-methods
findPeaks.centWave,xcmsRaw-method	findPeaks.centWave-methods
findPeaks.massifquant	findPeaks.massifquant-methods
findPeaks.massifquant,xcmsRaw-method	findPeaks.massifquant-methods
findPeaks.matchedFilter	findPeaks.matchedFilter-methods
findPeaks.matchedFilter,xcmsRaw-method	findPeaks.matchedFilter-methods
findPeaks.MS1	findPeaks.MS1-methods
findPeaks.MS1,xcmsRaw-method	findPeaks.MS1-methods
findPeaks.MSW	findPeaks.MSW-methods
findPeaks.MSW,xcmsRaw-method	findPeaks.MSW-methods
findRange	findEqualGreater
getEIC	getEIC-methods
getEIC,xcmsRaw-method	getEIC-methods
getEIC,xcmsSet-method	getEIC-methods
getMsnScan	getScan-methods
getMsnScan,xcmsRaw-method	getScan-methods
getPeaks	getPeaks-methods
getPeaks,xcmsRaw-method	getPeaks-methods
getScan	getScan-methods
getScan,xcmsRaw-method	getScan-methods
getSpec	getSpec-methods
getSpec,xcmsRaw-method	getSpec-methods
group	group-methods
group,xcmsSet-method	group-methods
group-methods	group-methods
group.density	group.density
group.density,xcmsSet-method	group.density
group.mzClust	group.mzClust
group.mzClust,xcmsSet-method	group.mzClust
group.nearest	group.nearest
group.nearest,xcmsSet-method	group.nearest
groupidx	xcmsSet-class
groupidx,xcmsSet-method	xcmsSet-class
groupidx<-	xcmsSet-class
groupidx<-,xcmsSet-method	xcmsSet-class
groupnames	groupnames-methods
groupnames,xcmsEIC-method	groupnames-methods
groupnames,xcmsSet-method	groupnames-methods
groups	xcmsSet-class
groups,xcmsSet-method	xcmsSet-class
groups<-	xcmsSet-class
groups<-,xcmsSet-method	xcmsSet-class
groupval	groupval-methods
groupval,xcmsSet-method	groupval-methods
image,xcmsRaw-method	image.xcmsRaw
initialize,netCdfSource-method	netCdfSource-class
initialize,rampSource-method	rampSource-class
integerMatrix	doubleMatrix
loadRaw	loadRaw-methods
loadRaw,netCdfSource-method	netCdfSource-class
loadRaw,rampSource-method	rampSource-class
loadRaw,xcmsSource-method	loadRaw-methods
loadRaw-methods	loadRaw-methods
logicalMatrix	doubleMatrix
makeacqNum	stitch-methods
makeacqNum, xcmsRaw-method	stitch-methods
medianFilter	medianFilter
mzrange	xcmsEIC-class
mzrange,xcmsEIC-method	xcmsEIC-class
na.flatfill	na.flatfill
netCDFClose	netCDF
netCDFIsFile	netCDF
netCDFMSPoints	netCDF
netCDFOpen	netCDF
netCDFRawData	netCDF
netCdfSource-class	netCdfSource-class
netCDFStrError	netCDF
netCDFVarDouble	netCDF
netCDFVarID	netCDF
netCDFVarInt	netCDF
netCDFVarLen	netCDF
panel.cor	panel.cor
peakPlots,xcmsSet-method	peakPlots-methods
peakPlots-methods	peakPlots-methods
peaks	xcmsSet-class
peaks,xcmsSet,missing-method	xcmsSet-class
peaks<-	xcmsSet-class
peaks<-,xcmsSet-method	xcmsSet-class
peakTable	peakTable-methods
peakTable,xcmsSet-method	peakTable-methods
phenoData	xcmsSet-class
phenoData,xcmsSet-method	xcmsSet-class
phenoData<-	xcmsSet-class
phenoData<-,xcmsSet-method	xcmsSet-class
plot, plot-methods	plot.xcmsEIC
plot.xcmsEIC	plot.xcmsEIC
plotChrom	plotChrom-methods
plotChrom,xcmsRaw-method	plotChrom-methods
plotEIC	plotEIC-methods
plotEIC,xcmsRaw-method	plotEIC-methods
plotPeaks	plotPeaks-methods
plotPeaks,xcmsRaw-method	plotPeaks-methods
plotRaw	plotRaw-methods
plotRaw,xcmsRaw-method	plotRaw-methods
plotrt	plotrt-methods
plotrt,xcmsSet-method	plotrt-methods
plotScan	plotScan-methods
plotScan,xcmsRaw-method	plotScan-methods
plotSpec	plotSpec-methods
plotSpec,xcmsRaw-method	plotSpec-methods
plotSurf	plotSurf-methods
plotSurf,xcmsRaw-method	plotSurf-methods
plotTIC	plotTIC-methods
plotTIC,xcmsRaw-method	plotTIC-methods
plotTree	xcmsFragments-class
plotTree,xcmsFragments-method	xcmsFragments-class
present	absent-methods
present,xcmsSet-method	absent-methods
profBin	profGenerate
profBinLin	profGenerate
profBinLinBase	profGenerate
profBinLinBaseM	profGenerate
profBinLinM	profGenerate
profBinM	profGenerate
profinfo	xcmsSet-class
profinfo,xcmsSet-method	xcmsSet-class
profinfo<-	xcmsSet-class
profinfo<-,xcmsSet-method	xcmsSet-class
profIntLin	profGenerate
profIntLinM	profGenerate
profMaxIdx	profGenerate
profMaxIdxM	profGenerate
profMedFilt	profMedFilt-methods
profMedFilt,xcmsRaw-method	profMedFilt-methods
profMethod	profMethod-methods
profMethod,xcmsRaw-method	profMethod-methods
profMethod<-	profMethod-methods
profMethod<-,xcmsRaw-method	profMethod-methods
profMz	xcmsRaw-class
profMz,xcmsRaw-method	xcmsRaw-class
profRange	profRange-methods
profRange,xcmsRaw-method	profRange-methods
profStep	profStep-methods
profStep,xcmsRaw-method	profStep-methods
profStep<-	profStep-methods
profStep<-,xcmsRaw-method	profStep-methods
progressCallback	xcmsSet-class
progressCallback,xcmsSet-method	xcmsSet-class
progressCallback<-	xcmsSet-class
progressCallback<-,xcmsSet-method	xcmsSet-class
pval	pval
rampClose	ramp
rampCloseAll	ramp
rampInit	ramp
rampIsFile	ramp
rampNumScans	ramp
rampOpen	ramp
rampPrintFiles	ramp
rampRawData	ramp
rampRawDataMSn	ramp
rampScanHeaders	ramp
rampSIPeaks	ramp
rampSource-class	rampSource-class
rawEIC	rawEIC-methods
rawEIC,xcmsRaw-method	rawEIC-methods
rawMat	rawMat-methods
rawMat,xcmsRaw-method	rawMat-methods
rawMat-methods	rawMat-methods
rectUnique	rectUnique
retcor	retcor-methods
retcor,xcmsSet-method	retcor-methods
retcor-methods	retcor-methods
retcor.linear	retcor.peakgroups-methods
retcor.linear,xcmsSet-method	retcor.peakgroups-methods
retcor.loess	retcor.peakgroups-methods
retcor.loess,xcmsSet-method	retcor.peakgroups-methods
retcor.obiwarp	retcor.obiwarp-methods
retcor.obiwarp,xcmsSet-method	retcor.obiwarp-methods
retcor.peakgroups	retcor.peakgroups-methods
retcor.peakgroups,xcmsSet-method	retcor.peakgroups-methods
retexp	retexp
revMz	xcmsRaw-class
revMz,xcmsRaw-method	xcmsRaw-class
rowMax	colMax
rtrange	xcmsEIC-class
rtrange,xcmsEIC-method	xcmsEIC-class
sampclass	xcmsSet-class
sampclass,xcmsSet-method	xcmsSet-class
sampclass<-	xcmsSet-class
sampclass<-,xcmsSet-method	xcmsSet-class
sampnames	sampnames-methods
sampnames,xcmsEIC-method	sampnames-methods
sampnames,xcmsSet-method	sampnames-methods
sampnames<-	xcmsSet-class
sampnames<-,xcmsSet-method	xcmsSet-class
show,xcmsEIC-method	xcmsEIC-class
show,xcmsFragments-method	xcmsFragments-class
show,xcmsPeaks-method	xcmsPeaks-class
show,xcmsRaw-method	xcmsRaw-class
show,xcmsSet-method	xcmsSet-class
sortMz	xcmsRaw-class
sortMz,xcmsRaw-method	xcmsRaw-class
specDist	specDist-methods
specDist,xcmsSet-method	specDist-methods
specDist-methods	specDist-methods
specDist.cosine	specDist.cosine-methods
specDist.cosine,matrix,matrix-method	specDist.cosine-methods
specDist.meanMZmatch	specDist.meanMZmatch-methods
specDist.meanMZmatch,matrix,matrix-method	specDist.meanMZmatch-methods
specDist.peakCount	specDist.peakCount-methods
specDist.peakCount,matrix,matrix-method	specDist.peakCount-methods
specDist.peakCount-methods	specDist.peakCount-methods
specNoise	specNoise
specPeaks	specPeaks
split, split-methods	split.xcmsSet
split.xcmsRaw	split.xcmsRaw
split.xcmsSet	split.xcmsSet
SSgauss	SSgauss
stitch	stitch-methods
stitch,xcmsRaw-method	stitch-methods
stitch-methods	stitch-methods
stitch.netCDF	stitch-methods
stitch.xml	stitch-methods
which.colMax	colMax
which.rowMax	colMax
write.cdf	write.cdf-methods
write.cdf,xcmsRaw-method	write.cdf-methods
write.mzdata	write.mzdata-methods
write.mzdata,xcmsRaw-method	write.mzdata-methods
xcmsEIC-class	xcmsEIC-class
xcmsFileSource-class	xcmsFileSource-class
xcmsFragments	xcmsFragments
xcmsFragments-class	xcmsFragments-class
xcmsPapply	xcmsPapply
xcmsPeaks-class	xcmsPeaks-class
xcmsRaw	xcmsRaw
xcmsRaw-class	xcmsRaw-class
xcmsSet	xcmsSet
xcmsSet-class	xcmsSet-class
xcmsSource	xcmsSource-methods
xcmsSource,character-method	xcmsFileSource-class
xcmsSource,xcmsSource-method	xcmsSource-methods
xcmsSource-class	xcmsSource-class
xcmsSource-methods	xcmsSource-methods
