MS Data Analysis

Global functions
AutoLockMass	Man page
AutoLockMass,xcmsRaw-method	Man page
AutoLockMass-methods	Man page
SSgauss	Man page
absent	Man page
absent,xcmsSet-method	Man page
c, c-methods	Man page
c.xcmsSet	Man page
calibrate	Man page
calibrate,xcmsSet-method	Man page
colMax	Man page
collect	Man page
collect,xcmsFragments-method	Man page
collect,xcmsRaw-method	Man page
collect-methods	Man page
deepCopy	Man page
deepCopy,xcmsRaw-method	Man page
descendMin	Man page
descendValue	Man page
descendZero	Man page
diffreport	Man page
diffreport,xcmsSet-method	Man page
doubleMatrix	Man page
etg	Man page
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
filtfft	Man page
findEqualGreater	Man page
findEqualGreaterM	Man page
findEqualLess	Man page
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
findRange	Man page
findneutral	Man page
findneutral,xcmsFragments-method	Man page
getEIC	Man page
getEIC,xcmsRaw-method	Man page
getEIC,xcmsSet-method	Man page
getEIC-methods	Man page
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
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
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
makeacqNum	Man page
makeacqNum, xcmsRaw-method	Man page
medianFilter	Man page
msn2xcmsRaw	Man page
mzrange	Man page
mzrange,xcmsEIC-method	Man page
na.flatfill	Man page
netCDFClose	Man page
netCDFIsFile	Man page
netCDFMSPoints	Man page
netCDFOpen	Man page
netCDFRawData	Man page
netCDFStrError	Man page
netCDFVarDouble	Man page
netCDFVarID	Man page
netCDFVarInt	Man page
netCDFVarLen	Man page
netCdfSource-class	Man page
panel.cor	Man page
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
plot, plot-methods	Man page
plot.xcmsEIC	Man page
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
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
present	Man page
present,xcmsSet-method	Man page
profBin	Man page
profBinLin	Man page
profBinLinBase	Man page
profBinLinBaseM	Man page
profBinLinM	Man page
profBinM	Man page
profIntLin	Man page
profIntLinM	Man page
profMaxIdx	Man page
profMaxIdxM	Man page
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
rampClose	Man page
rampCloseAll	Man page
rampInit	Man page
rampIsFile	Man page
rampNumScans	Man page
rampOpen	Man page
rampPrintFiles	Man page
rampRawData	Man page
rampRawDataMSn	Man page
rampSIPeaks	Man page
rampScanHeaders	Man page
rampSource-class	Man page
rawEIC	Man page
rawEIC,xcmsRaw-method	Man page
rawMat	Man page
rawMat,xcmsRaw-method	Man page
rawMat-methods	Man page
rectUnique	Man page
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
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
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
specPeaks	Man page
split, split-methods	Man page
split.xcmsRaw	Man page
split.xcmsSet	Man page
stitch	Man page
stitch,xcmsRaw-method	Man page
stitch-methods	Man page
stitch.netCDF	Man page
stitch.xml	Man page
verify.mzQuantML	Man page
which.colMax	Man page
which.rowMax	Man page
write.cdf	Man page
write.cdf,xcmsRaw-method	Man page
write.mzQuantML	Man page
write.mzQuantML,xcmsSet-method	Man page
write.mzdata	Man page
write.mzdata,xcmsRaw-method	Man page
xcmsEIC-class	Man page
xcmsFileSource-class	Man page
xcmsFragments	Man page
xcmsFragments-class	Man page
xcmsPapply	Man page
xcmsPeaks-class	Man page
xcmsRaw	Man page
xcmsRaw-class	Man page
xcmsSet	Man page
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