MS Data Analysis

Global functions
.onLoad	Source code Source code
.onUnload	Source code Source code
.setXCMSOptions	Source code
.xcmsFragments.collect	Source code
.xcmsFragments.hasMSn	Source code
.xcmsFragments.plotTree	Source code
.xcmsFragments.show	Source code
AutoLockMass	Man page
AutoLockMass,xcmsRaw-method	Man page
AutoLockMass-methods	Man page
KeggSearch	Source code
MSW.extendLength	Source code
MSW.extendNBase	Source code
MSW.getLocalMaximumCWT	Source code
MSW.getRidge	Source code
SSgauss	Man page
absent	Man page
absent,xcmsSet-method	Man page
c, c-methods	Man page
c.xcmsSet	Man page Source code
calibrate	Man page
calibrate,xcmsSet-method	Man page
cent	Source code
colMax	Man page
collect	Man page
collect,xcmsFragments-method	Man page
collect,xcmsRaw-method	Man page
collect-methods	Man page
continuousPtsAboveThreshold	Source code
continuousPtsAboveThresholdIdx	Source code
deepCopy	Man page
deepCopy,xcmsRaw-method	Man page
descendMin	Man page Source code
descendMinTol	Source code
descendValue	Man page Source code
descendZero	Man page Source code
diffreport	Man page
diffreport,xcmsSet-method	Man page
doubleMatrix	Man page Source code
estimate	Source code
estimateChromNoise	Source code
etg	Man page Source code
fastMatch	Source code
filepaths	Man page
filepaths,xcmsSet-method	Man page
filepaths<-	Man page
filepaths<-,xcmsSet-method	Man page
fillPeaks	Man page
fillPeaks,xcmsSet-method	Man page
fillPeaks-methods	Man page
fillPeaks.MSW	Man page
fillPeaks.MSW,xcmsSet-method	Man page
fillPeaks.MSW-methods	Man page
fillPeaks.chrom	Man page
fillPeaks.chrom,xcmsSet-method	Man page
fillPeaks.chrom-methods	Man page
fillPeaksChromPar	Source code
filtfft	Man page Source code
findEqualGreater	Man page Source code
findEqualGreaterM	Man page Source code
findEqualGreaterUnsorted	Source code
findEqualLess	Man page Source code
findMZ	Man page
findMZ,xcmsFragments-method	Man page
findPeaks	Man page
findPeaks,xcmsRaw-method	Man page
findPeaks-methods	Man page
findPeaks.MS1	Man page
findPeaks.MS1,xcmsRaw-method	Man page
findPeaks.MSW	Man page
findPeaks.MSW,xcmsRaw-method	Man page
findPeaks.centWave	Man page
findPeaks.centWave,xcmsRaw-method	Man page
findPeaks.massifquant	Man page
findPeaks.massifquant,xcmsRaw-method	Man page
findPeaks.matchedFilter	Man page
findPeaks.matchedFilter,xcmsRaw-method	Man page
findPeaksPar	Source code
findRange	Man page Source code
findneutral	Man page
findneutral,xcmsFragments-method	Man page
fitGauss	Source code
gauss	Source code
gaussCoverage	Source code
getEIC	Man page
getEIC,xcmsRaw-method	Man page
getEIC,xcmsSet-method	Man page
getEIC-methods	Man page
getLocalNoiseEstimate	Source code
getMsnScan	Man page
getMsnScan,xcmsRaw-method	Man page
getPeaks	Man page
getPeaks,xcmsRaw-method	Man page
getPeaks-methods	Man page
getScan	Man page
getScan,xcmsRaw-method	Man page
getSpec	Man page
getSpec,xcmsRaw-method	Man page
getSpec-methods	Man page
getSpecWindow	Source code
getXS	Source code
group	Man page
group,xcmsSet-method	Man page
group-methods	Man page
group.density	Man page
group.density,xcmsSet-method	Man page
group.mzClust	Man page
group.mzClust,xcmsSet-method	Man page
group.nearest	Man page
group.nearest,xcmsSet-method	Man page
groupidx	Man page
groupidx,xcmsSet-method	Man page
groupidx<-	Man page
groupidx<-,xcmsSet-method	Man page
groupnames	Man page
groupnames,xcmsEIC-method	Man page
groupnames,xcmsSet-method	Man page
groupnames-methods	Man page
groups	Man page
groups,xcmsSet-method	Man page
groups<-	Man page
groups<-,xcmsSet-method	Man page
groupval	Man page
groupval,xcmsSet-method	Man page
groupval-methods	Man page
image,xcmsRaw-method	Man page
initialize,netCdfSource-method	Man page
initialize,rampSource-method	Man page
integerMatrix	Man page Source code
joinOverlappingPeaks	Source code
loadRaw	Man page
loadRaw,netCdfSource-method	Man page
loadRaw,rampSource-method	Man page
loadRaw,xcmsSource-method	Man page
loadRaw-methods	Man page
logicalMatrix	Man page Source code
makeacqNum	Man page
makeacqNum, xcmsRaw-method	Man page
match.profFun	Source code
matchpeaks	Source code
medianFilter	Man page Source code
minifm	Source code
msgfun.featureDetection	Source code
msgfunGeneric	Source code
msn2xcmsRaw	Man page Source code
mzCenter.apex	Source code
mzCenter.mean	Source code
mzCenter.meanApex3	Source code
mzCenter.wMean	Source code
mzCenter.wMeanApex3	Source code
mzClustGeneric	Source code
mzClust_hclust	Source code
mzRRawData	Source code
mzRRawDataMSn	Source code
mzrange	Man page
mzrange,xcmsEIC-method	Man page
na.flatfill	Man page Source code
netCDFClose	Man page Source code
netCDFIsFile	Man page Source code
netCDFMSPoints	Man page Source code
netCDFOpen	Man page Source code
netCDFRawData	Man page Source code
netCDFStrError	Man page Source code
netCDFVarDouble	Man page Source code
netCDFVarID	Man page Source code
netCDFVarInt	Man page Source code
netCDFVarLen	Man page Source code
netCdfSource-class	Man page
panel.cor	Man page Source code
patternVsRowScore	Source code
peakPlots,xcmsSet-method	Man page
peakPlots-methods	Man page
peakTable	Man page
peakTable,xcmsSet-method	Man page
peaks	Man page
peaks,xcmsSet,missing-method	Man page
peaks<-	Man page
peaks<-,xcmsSet-method	Man page
phenoData	Man page
phenoData,xcmsSet-method	Man page
phenoData<-	Man page
phenoData<-,xcmsSet-method	Man page
phenoDataFromPaths	Source code
plot, plot-methods	Man page
plot.xcmsEIC	Man page Source code
plotChrom	Man page
plotChrom,xcmsRaw-method	Man page
plotChrom-methods	Man page
plotEIC	Man page
plotEIC,xcmsRaw-method	Man page
plotPeaks	Man page
plotPeaks,xcmsRaw-method	Man page
plotPeaks-methods	Man page
plotRaw	Man page
plotRaw,xcmsRaw-method	Man page
plotRaw-methods	Man page
plotScan	Man page
plotScan,xcmsRaw-method	Man page
plotScan-methods	Man page
plotSpec	Man page
plotSpec,xcmsRaw-method	Man page
plotSpec-methods	Man page
plotSpecWindow	Source code
plotSurf	Man page
plotSurf,xcmsRaw-method	Man page
plotSurf-methods	Man page
plotTIC	Man page
plotTIC,xcmsRaw-method	Man page
plotTIC-methods	Man page
plotTree	Man page
plotTree,xcmsFragments-method	Man page
plotrt	Man page
plotrt,xcmsSet-method	Man page
plotrt-methods	Man page
ppm	Source code
ppmDev	Source code
present	Man page
present,xcmsSet-method	Man page
profBin	Man page Source code
profBinLin	Man page Source code
profBinLinBase	Man page Source code
profBinLinBaseM	Man page Source code
profBinLinM	Man page Source code
profBinM	Man page Source code
profIntLin	Man page Source code
profIntLinM	Man page Source code
profMaxIdx	Man page Source code
profMaxIdxM	Man page Source code
profMedFilt	Man page
profMedFilt,xcmsRaw-method	Man page
profMedFilt-methods	Man page
profMethod	Man page
profMethod,xcmsRaw-method	Man page
profMethod-methods	Man page
profMethod<-	Man page
profMethod<-,xcmsRaw-method	Man page
profMethod<--methods	Man page
profMz	Man page
profMz,xcmsRaw-method	Man page
profRange	Man page
profRange,xcmsRaw-method	Man page
profRange-methods	Man page
profStep	Man page
profStep,xcmsRaw-method	Man page
profStep-methods	Man page
profStep<-	Man page
profStep<-,xcmsRaw-method	Man page
profStep<--methods	Man page
profinfo	Man page
profinfo,xcmsSet-method	Man page
profinfo<-	Man page
profinfo<-,xcmsSet-method	Man page
progressCallback	Man page
progressCallback,xcmsSet-method	Man page
progressCallback<-	Man page
progressCallback<-,xcmsSet-method	Man page
pval	Man page Source code
rampClose	Man page Source code
rampCloseAll	Man page Source code
rampInit	Man page Source code
rampIsFile	Man page Source code
rampNumScans	Man page Source code
rampOpen	Man page Source code
rampPrintFiles	Man page Source code
rampRawData	Man page Source code
rampRawDataMSn	Man page Source code
rampSIPeaks	Man page Source code
rampScanHeaders	Man page Source code
rampSource-class	Man page
rawEIC	Man page
rawEIC,xcmsRaw-method	Man page
rawMat	Man page
rawMat,xcmsRaw-method	Man page
rawMat-methods	Man page
read.mascot	Source code
rectUnique	Man page Source code
remakeTIC	Source code
retcor	Man page
retcor,xcmsSet-method	Man page
retcor-methods	Man page
retcor.linear	Man page
retcor.linear,xcmsSet-method	Man page
retcor.loess	Man page
retcor.loess,xcmsSet-method	Man page
retcor.obiwarp	Man page
retcor.obiwarp,xcmsSet-method	Man page
retcor.peakgroups	Man page
retcor.peakgroups,xcmsSet-method	Man page
retexp	Man page Source code
revMz	Man page
revMz,xcmsRaw-method	Man page
rowMax	Man page
rtrange	Man page
rtrange,xcmsEIC-method	Man page
sampclass	Man page
sampclass,xcmsSet-method	Man page
sampclass<-	Man page
sampclass<-,xcmsSet-method	Man page
sampnames	Man page
sampnames,xcmsEIC-method	Man page
sampnames,xcmsSet-method	Man page
sampnames-methods	Man page
sampnames<-	Man page
sampnames<-,xcmsSet-method	Man page
sequences	Source code
show,xcmsEIC-method	Man page
show,xcmsFragments-method	Man page
show,xcmsPeaks-method	Man page
show,xcmsRaw-method	Man page
show,xcmsSet-method	Man page
sortMz	Man page
sortMz,xcmsRaw-method	Man page
specDist	Man page
specDist,xcmsSet-method	Man page
specDist-methods	Man page
specDist.cosine	Man page
specDist.cosine,matrix,matrix-method	Man page
specDist.meanMZmatch	Man page
specDist.meanMZmatch,matrix,matrix-method	Man page
specDist.peakCount	Man page
specDist.peakCount,matrix,matrix-method	Man page
specDist.peakCount-methods	Man page
specNoise	Man page Source code
specPeaks	Man page Source code
split, split-methods	Man page
split.xcmsRaw	Man page Source code
split.xcmsSet	Man page Source code
stitch	Man page
stitch,xcmsRaw-method	Man page
stitch-methods	Man page
stitch.netCDF	Man page
stitch.xml	Man page
trimm	Source code
which.colMax	Man page
which.rowMax	Man page
write.cdf	Man page
write.cdf,xcmsRaw-method	Man page
write.mzdata	Man page
write.mzdata,xcmsRaw-method	Man page
xcmsBoxPlot	Source code
xcmsClusterApply	Source code
xcmsEIC-class	Man page
xcmsFileSource-class	Man page
xcmsFragments	Man page Source code
xcmsFragments-class	Man page
xcmsFragments.makeXS	Source code
xcmsPapply	Man page
xcmsParallelSetup	Source code
xcmsPeaks-class	Man page
xcmsRaw	Man page Source code
xcmsRaw-class	Man page
xcmsSet	Man page Source code
xcmsSet-class	Man page
xcmsSource	Man page
xcmsSource,character-method	Man page
xcmsSource,xcmsSource-method	Man page
xcmsSource-class	Man page
xcmsSource-methods	Man page