LC/MS and GC/MS Data Analysis


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Documentation for package ‘xcms’ version 1.52.0

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A B C D E F G H I K L M N O P R S T U V W X misc

-- A --

absent Determine which peaks are absent / present in a sample class
absent-method Determine which peaks are absent / present in a sample class
absMz High resolution peak grouping for single spectra samples
absMz-method High resolution peak grouping for single spectra samples
absMz-method Peak grouping based on proximity in the mz-rt space
absMz<- High resolution peak grouping for single spectra samples
absMz<--method High resolution peak grouping for single spectra samples
absMz<--method Peak grouping based on proximity in the mz-rt space
absRt Peak grouping based on proximity in the mz-rt space
absRt-method Peak grouping based on proximity in the mz-rt space
absRt<- Peak grouping based on proximity in the mz-rt space
absRt<--method Peak grouping based on proximity in the mz-rt space
addParams Single-spectrum non-chromatography MS data peak detection
addParams-method Single-spectrum non-chromatography MS data peak detection
addParams<- Single-spectrum non-chromatography MS data peak detection
addParams<--method Single-spectrum non-chromatography MS data peak detection
adjustedRtime Data container storing xcms preprocessing results
adjustedRtime-method Data container storing xcms preprocessing results
adjustedRtime<- Data container storing xcms preprocessing results
adjustedRtime<--method Data container storing xcms preprocessing results
adjustRtime Alignment: Retention time correction methods.
adjustRtime-method Align retention times across samples using Obiwarp
adjustRtime-method Retention time correction based on alignment of house keeping peak groups
adjustRtime-obiwarp Align retention times across samples using Obiwarp
adjustRtime-peakGroups Retention time correction based on alignment of house keeping peak groups
adjustRtimePeakGroups Retention time correction based on alignment of house keeping peak groups
aggregationFun Representation of chromatographic MS data
aggregationFun-method Representation of chromatographic MS data
ampTh Single-spectrum non-chromatography MS data peak detection
ampTh-method Single-spectrum non-chromatography MS data peak detection
ampTh<- Single-spectrum non-chromatography MS data peak detection
ampTh<--method Single-spectrum non-chromatography MS data peak detection
as.data.frame-method Representation of chromatographic MS data
AutoLockMass Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-method Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-methods Automatic parameter for Lock mass fixing 'AutoLockMass' ~~

-- B --

baseValue Peak detection in the chromatographic time domain
baseValue-method Peak detection in the chromatographic time domain
baseValue<- Peak detection in the chromatographic time domain
baseValue<--method Peak detection in the chromatographic time domain
bin-method XCMSnExp data manipulation methods inherited from MSnbase
binSize Peak detection in the chromatographic time domain
binSize-method Align retention times across samples using Obiwarp
binSize-method Peak detection in the chromatographic time domain
binSize-method Peak grouping based on time dimension peak densities
binSize<- Peak detection in the chromatographic time domain
binSize<--method Align retention times across samples using Obiwarp
binSize<--method Peak detection in the chromatographic time domain
binSize<--method Peak grouping based on time dimension peak densities
binYonX Aggregate values in y for bins defined on x
breaks_on_binSize Generate breaks for binning using a defined bin size.
breaks_on_nBins Generate breaks for binning
bw Peak grouping based on time dimension peak densities
bw-method Peak grouping based on time dimension peak densities
bw<- Peak grouping based on time dimension peak densities
bw<--method Peak grouping based on time dimension peak densities

-- C --

c, c-methods Combine xcmsSet objects
c.xcmsSet Combine xcmsSet objects
calibrate Calibrate peaks for correcting unprecise m/z values
calibrate-method Calibrate peaks for correcting unprecise m/z values
centerSample Align retention times across samples using Obiwarp
centerSample-method Align retention times across samples using Obiwarp
centerSample<- Align retention times across samples using Obiwarp
centerSample<--method Align retention times across samples using Obiwarp
centWave Chromatographic peak detection using the centWave method
CentWaveParam Chromatographic peak detection using the centWave method
CentWaveParam-class Chromatographic peak detection using the centWave method
CentWavePredIsoParam Two-step centWave peak detection considering also isotopes
CentWavePredIsoParam-class Two-step centWave peak detection considering also isotopes
centWaveWithPredIsoROIs Two-step centWave peak detection considering also isotopes
checkBack Chromatographic peak detection using the massifquant method
checkBack-method Chromatographic peak detection using the massifquant method
checkBack<- Chromatographic peak detection using the massifquant method
checkBack<--method Chromatographic peak detection using the massifquant method
Chromatogram Representation of chromatographic MS data
Chromatogram-class Representation of chromatographic MS data
chromatographic-peak-detection Chromatographic peak detection methods.
chromPeaks Data container storing xcms preprocessing results
chromPeaks-method Data container storing xcms preprocessing results
chromPeaks<- Data container storing xcms preprocessing results
chromPeaks<--method Data container storing xcms preprocessing results
clean-method XCMSnExp data manipulation methods inherited from MSnbase
collect Collect MS^n peaks into xcmsFragments
collect-method Collect MS^n peaks into xcmsFragments
collect-methods Collect MS^n peaks into xcmsFragments
consecMissedLimit Chromatographic peak detection using the massifquant method
consecMissedLimit-method Chromatographic peak detection using the massifquant method
consecMissedLimit<- Chromatographic peak detection using the massifquant method
consecMissedLimit<--method Chromatographic peak detection using the massifquant method
criticalValue Chromatographic peak detection using the massifquant method
criticalValue-method Chromatographic peak detection using the massifquant method
criticalValue<- Chromatographic peak detection using the massifquant method
criticalValue<--method Chromatographic peak detection using the massifquant method

-- D --

deepCopy Constructor for xcmsRaw objects which reads NetCDF/mzXML files
deepCopy-method Constructor for xcmsRaw objects which reads NetCDF/mzXML files
diffreport Create report of analyte differences
diffreport-method Create report of analyte differences
distance Peak detection in the chromatographic time domain
distance-method Peak detection in the chromatographic time domain
distance<- Peak detection in the chromatographic time domain
distance<--method Peak detection in the chromatographic time domain
distFun Align retention times across samples using Obiwarp
distFun-method Align retention times across samples using Obiwarp
distFun<- Align retention times across samples using Obiwarp
distFun<--method Align retention times across samples using Obiwarp
do_adjustRtime_peakGroups Align spectrum retention times across samples using peak groups found in most samples
do_findChromPeaks_addPredIsoROIs Core API function for two-step centWave peak detection with isotopes
do_findChromPeaks_centWave Core API function for centWave peak detection
do_findChromPeaks_centWaveWithPredIsoROIs Core API function for two-step centWave peak detection with isotopes
do_findChromPeaks_massifquant Core API function for massifquant peak detection
do_findChromPeaks_matchedFilter Core API function for matchedFilter peak detection
do_findPeaks_MSW Core API function for single-spectrum non-chromatography MS data peak detection
do_groupChromPeaks_density Core API function for peak density based chromatographic peak grouping
do_groupChromPeaks_nearest Core API function for chromatic peak grouping using a nearest neighbor approach
do_groupPeaks_mzClust Core API function for peak grouping using mzClust
dropAdjustedRtime Data container storing xcms preprocessing results
dropAdjustedRtime-method Data container storing xcms preprocessing results
dropChromPeaks Data container storing xcms preprocessing results
dropChromPeaks-method Data container storing xcms preprocessing results
dropFeatureDefinitions Data container storing xcms preprocessing results
dropFeatureDefinitions-method Data container storing xcms preprocessing results
dropFilledChromPeaks Data container storing xcms preprocessing results
dropFilledChromPeaks-method Data container storing xcms preprocessing results

-- E --

etg Empirically Transformed Gaussian function
expandMz Integrate areas of missing peaks
expandMz-method Integrate areas of missing peaks
expandMz<- Integrate areas of missing peaks
expandMz<--method Integrate areas of missing peaks
expandRt Integrate areas of missing peaks
expandRt-method Integrate areas of missing peaks
expandRt<- Integrate areas of missing peaks
expandRt<--method Integrate areas of missing peaks
extractChromatograms Extracting chromatograms
extractChromatograms-method Extracting chromatograms
extraPeaks Retention time correction based on alignment of house keeping peak groups
extraPeaks-method Retention time correction based on alignment of house keeping peak groups
extraPeaks<- Retention time correction based on alignment of house keeping peak groups
extraPeaks<--method Retention time correction based on alignment of house keeping peak groups

-- F --

factorDiag Align retention times across samples using Obiwarp
factorDiag-method Align retention times across samples using Obiwarp
factorDiag<- Align retention times across samples using Obiwarp
factorDiag<--method Align retention times across samples using Obiwarp
factorGap Align retention times across samples using Obiwarp
factorGap-method Align retention times across samples using Obiwarp
factorGap<- Align retention times across samples using Obiwarp
factorGap<--method Align retention times across samples using Obiwarp
family Retention time correction based on alignment of house keeping peak groups
family-method Retention time correction based on alignment of house keeping peak groups
family<- Retention time correction based on alignment of house keeping peak groups
family<--method Retention time correction based on alignment of house keeping peak groups
featureDefinitions Data container storing xcms preprocessing results
featureDefinitions-method Data container storing xcms preprocessing results
featureDefinitions<- Data container storing xcms preprocessing results
featureDefinitions<--method Data container storing xcms preprocessing results
featureValues Accessing mz-rt feature data values
featureValues-method Accessing mz-rt feature data values
fileIndex Tracking data processing
fileIndex-method Tracking data processing
filepaths Class xcmsSet, a class for preprocessing peak data
filepaths-method Class xcmsSet, a class for preprocessing peak data
filepaths<- Class xcmsSet, a class for preprocessing peak data
filepaths<--method Class xcmsSet, a class for preprocessing peak data
fillChromPeaks Integrate areas of missing peaks
fillChromPeaks-method Integrate areas of missing peaks
FillChromPeaksParam Integrate areas of missing peaks
FillChromPeaksParam-class Integrate areas of missing peaks
fillPeaks Integrate areas of missing peaks
fillPeaks-method Integrate areas of missing peaks
fillPeaks.chrom Integrate areas of missing peaks
fillPeaks.chrom-method Integrate areas of missing peaks
fillPeaks.MSW Integrate areas of missing peaks in FTICR-MS data
fillPeaks.MSW-method Integrate areas of missing peaks in FTICR-MS data
filterAcquisitionNum-method XCMSnExp data manipulation methods inherited from MSnbase
filterFile-method XCMSnExp filtering and subsetting
filterMsLevel-method XCMSnExp data manipulation methods inherited from MSnbase
filterMz-method XCMSnExp filtering and subsetting
filterRt-method Representation of chromatographic MS data
filterRt-method XCMSnExp filtering and subsetting
findChromPeaks Chromatographic peak detection methods.
findChromPeaks-centWave Chromatographic peak detection using the centWave method
findChromPeaks-centWaveWithPredIsoROIs Two-step centWave peak detection considering also isotopes
findChromPeaks-massifquant Chromatographic peak detection using the massifquant method
findChromPeaks-matchedFilter Peak detection in the chromatographic time domain
findChromPeaks-method Data container storing xcms preprocessing results
findChromPeaks-method Chromatographic peak detection using the centWave method
findChromPeaks-method Two-step centWave peak detection considering also isotopes
findChromPeaks-method Chromatographic peak detection using the massifquant method
findChromPeaks-method Peak detection in the chromatographic time domain
findChromPeaks-method Single-spectrum non-chromatography MS data peak detection
findMZ Find fragment ions in xcmsFragment objects
findMZ-method Find fragment ions in xcmsFragment objects
findneutral Find neutral losses in xcmsFragment objects
findneutral-method Find neutral losses in xcmsFragment objects
findPeaks Feature detection for GC/MS and LC/MS Data - methods
findPeaks-method Feature detection for GC/MS and LC/MS Data - methods
findPeaks-methods Feature detection for GC/MS and LC/MS Data - methods
findPeaks-MSW Single-spectrum non-chromatography MS data peak detection
findPeaks.addPredictedIsotopeFeatures Feature detection based on predicted isotope features for high resolution LC/MS data
findPeaks.addPredictedIsotopeFeatures-method Feature detection based on predicted isotope features for high resolution LC/MS data
findPeaks.centWave Feature detection for high resolution LC/MS data
findPeaks.centWave-method Feature detection for high resolution LC/MS data
findPeaks.centWaveWithPredictedIsotopeROIs Feature detection with centWave and additional isotope features
findPeaks.centWaveWithPredictedIsotopeROIs-method Feature detection with centWave and additional isotope features
findPeaks.massifquant Feature detection for XC-MS data.
findPeaks.massifquant-method Feature detection for XC-MS data.
findPeaks.matchedFilter Peak detection in the chromatographic time domain
findPeaks.matchedFilter-method Peak detection in the chromatographic time domain
findPeaks.MS1 Collecting MS1 precursor peaks
findPeaks.MS1-method Collecting MS1 precursor peaks
findPeaks.MSW Peak detection for single-spectrum non-chromatography MS data
findPeaks.MSW-method Peak detection for single-spectrum non-chromatography MS data
firstBaselineCheck Chromatographic peak detection using the centWave method
firstBaselineCheck-method Chromatographic peak detection using the centWave method
firstBaselineCheck<- Chromatographic peak detection using the centWave method
firstBaselineCheck<--method Chromatographic peak detection using the centWave method
fitgauss Chromatographic peak detection using the centWave method
fitgauss-method Chromatographic peak detection using the centWave method
fitgauss-method Chromatographic peak detection using the massifquant method
fitgauss<- Chromatographic peak detection using the centWave method
fitgauss<--method Chromatographic peak detection using the centWave method
fitgauss<--method Chromatographic peak detection using the massifquant method
fromFile-method Representation of chromatographic MS data
fwhm Peak detection in the chromatographic time domain
fwhm-method Peak detection in the chromatographic time domain
fwhm<- Peak detection in the chromatographic time domain
fwhm<--method Peak detection in the chromatographic time domain

-- G --

gapExtend Align retention times across samples using Obiwarp
gapExtend-method Align retention times across samples using Obiwarp
gapExtend<- Align retention times across samples using Obiwarp
gapExtend<--method Align retention times across samples using Obiwarp
gapInit Align retention times across samples using Obiwarp
gapInit-method Align retention times across samples using Obiwarp
gapInit<- Align retention times across samples using Obiwarp
gapInit<--method Align retention times across samples using Obiwarp
GenericParam Generic parameter class
GenericParam-class Generic parameter class
getEIC Get extracted ion chromatograms for specified m/z ranges
getEIC-method Get extracted ion chromatograms for specified m/z ranges
getMsnScan Get m/z and intensity values for a single mass scan
getMsnScan-method Get m/z and intensity values for a single mass scan
getPeaks Get peak intensities for specified regions
getPeaks-method Get peak intensities for specified regions
getScan Get m/z and intensity values for a single mass scan
getScan-method Get m/z and intensity values for a single mass scan
getSpec Get average m/z and intensity values for multiple mass scans
getSpec-method Get average m/z and intensity values for multiple mass scans
getXcmsRaw Load the raw data for one or more files in the xcmsSet
getXcmsRaw-method Load the raw data for one or more files in the xcmsSet
group Group peaks from different samples together
group-method Group peaks from different samples together
group-methods Group peaks from different samples together
group.density Group peaks from different samples together
group.density-method Group peaks from different samples together
group.mzClust Group Peaks via High Resolution Alignment
group.mzClust-method Group Peaks via High Resolution Alignment
group.nearest Group peaks from different samples together
group.nearest-method Group peaks from different samples together
groupChromPeaks Correspondence: Chromatographic peak grouping methods.
groupChromPeaks-density Peak grouping based on time dimension peak densities
groupChromPeaks-method Peak grouping based on time dimension peak densities
groupChromPeaks-method High resolution peak grouping for single spectra samples
groupChromPeaks-method Peak grouping based on proximity in the mz-rt space
groupChromPeaks-mzClust High resolution peak grouping for single spectra samples
groupChromPeaks-nearest Peak grouping based on proximity in the mz-rt space
groupidx Class xcmsSet, a class for preprocessing peak data
groupidx-method Class xcmsSet, a class for preprocessing peak data
groupidx<- Class xcmsSet, a class for preprocessing peak data
groupidx<--method Class xcmsSet, a class for preprocessing peak data
groupnames Generate unque names for peak groups
groupnames-method Generate unque names for peak groups
groups Class xcmsSet, a class for preprocessing peak data
groups-method Class xcmsSet, a class for preprocessing peak data
groups<- Class xcmsSet, a class for preprocessing peak data
groups<--method Class xcmsSet, a class for preprocessing peak data
groupval Extract a matrix of peak values for each group
groupval-method Extract a matrix of peak values for each group

-- H --

hasAdjustedRtime Data container storing xcms preprocessing results
hasAdjustedRtime-method Data container storing xcms preprocessing results
hasChromPeaks Data container storing xcms preprocessing results
hasChromPeaks-method Data container storing xcms preprocessing results
hasFeatures Data container storing xcms preprocessing results
hasFeatures-method Data container storing xcms preprocessing results

-- I --

image-method Plot log intensity image of a xcmsRaw object
impute-method Peak detection in the chromatographic time domain
impute<- Peak detection in the chromatographic time domain
impute<--method Peak detection in the chromatographic time domain
imputeLinInterpol Impute values for empty elements in a vector using linear interpolation
index Peak detection in the chromatographic time domain
index-method Peak detection in the chromatographic time domain
index<- Peak detection in the chromatographic time domain
index<--method Peak detection in the chromatographic time domain
initPenalty Align retention times across samples using Obiwarp
initPenalty-method Align retention times across samples using Obiwarp
initPenalty<- Align retention times across samples using Obiwarp
initPenalty<--method Align retention times across samples using Obiwarp
integrate-method Chromatographic peak detection using the centWave method
integrate-method Chromatographic peak detection using the massifquant method
integrate<- Chromatographic peak detection using the centWave method
integrate<--method Chromatographic peak detection using the centWave method
integrate<--method Chromatographic peak detection using the massifquant method
intensity-method Representation of chromatographic MS data
intensity-method Data container storing xcms preprocessing results

-- K --

kNN Peak grouping based on proximity in the mz-rt space
kNN-method Peak grouping based on proximity in the mz-rt space
kNN<- Peak grouping based on proximity in the mz-rt space
kNN<--method Peak grouping based on proximity in the mz-rt space

-- L --

length-method Representation of chromatographic MS data
levelplot Class xcmsRaw, a class for handling raw data
levelplot-method Plot log intensity image of a xcmsRaw object
loadRaw Read binary data from a source
loadRaw-method Read binary data from a source
loadRaw-methods Read binary data from a source
localAlignment Align retention times across samples using Obiwarp
localAlignment-method Align retention times across samples using Obiwarp
localAlignment<- Align retention times across samples using Obiwarp
localAlignment<--method Align retention times across samples using Obiwarp

-- M --

makeacqNum Correct gaps in data
makeacqNum-method Correct gaps in data
massifquant Chromatographic peak detection using the massifquant method
MassifquantParam Chromatographic peak detection using the massifquant method
MassifquantParam-class Chromatographic peak detection using the massifquant method
matchedFilter Peak detection in the chromatographic time domain
MatchedFilterParam Peak detection in the chromatographic time domain
MatchedFilterParam-class Peak detection in the chromatographic time domain
max-method Peak detection in the chromatographic time domain
max<- Peak detection in the chromatographic time domain
max<--method Peak detection in the chromatographic time domain
maxCharge Two-step centWave peak detection considering also isotopes
maxCharge-method Two-step centWave peak detection considering also isotopes
maxCharge<- Two-step centWave peak detection considering also isotopes
maxCharge<--method Two-step centWave peak detection considering also isotopes
maxFeatures Peak grouping based on time dimension peak densities
maxFeatures-method Peak grouping based on time dimension peak densities
maxFeatures<- Peak grouping based on time dimension peak densities
maxFeatures<--method Peak grouping based on time dimension peak densities
maxIso Two-step centWave peak detection considering also isotopes
maxIso-method Two-step centWave peak detection considering also isotopes
maxIso<- Two-step centWave peak detection considering also isotopes
maxIso<--method Two-step centWave peak detection considering also isotopes
medianFilter Apply a median filter to a matrix
minFraction Peak grouping based on time dimension peak densities
minFraction-method Retention time correction based on alignment of house keeping peak groups
minFraction-method Peak grouping based on time dimension peak densities
minFraction-method High resolution peak grouping for single spectra samples
minFraction<- Peak grouping based on time dimension peak densities
minFraction<--method Retention time correction based on alignment of house keeping peak groups
minFraction<--method Peak grouping based on time dimension peak densities
minFraction<--method High resolution peak grouping for single spectra samples
minNoiseLevel Single-spectrum non-chromatography MS data peak detection
minNoiseLevel-method Single-spectrum non-chromatography MS data peak detection
minNoiseLevel<- Single-spectrum non-chromatography MS data peak detection
minNoiseLevel<--method Single-spectrum non-chromatography MS data peak detection
minSamples Peak grouping based on time dimension peak densities
minSamples-method Peak grouping based on time dimension peak densities
minSamples-method High resolution peak grouping for single spectra samples
minSamples<- Peak grouping based on time dimension peak densities
minSamples<--method Peak grouping based on time dimension peak densities
minSamples<--method High resolution peak grouping for single spectra samples
MsFeatureData Data container storing xcms preprocessing results
MsFeatureData-class Data container storing xcms preprocessing results
mslevel Class xcmsSet, a class for preprocessing peak data
mslevel-method Class xcmsRaw, a class for handling raw data
mslevel-method Class xcmsSet, a class for preprocessing peak data
msn2xcmsRaw Copy MSn data in an xcmsRaw to the MS slots
MSW Single-spectrum non-chromatography MS data peak detection
MSWParam Single-spectrum non-chromatography MS data peak detection
MSWParam-class Single-spectrum non-chromatography MS data peak detection
mz-method Representation of chromatographic MS data
mz-method Data container storing xcms preprocessing results
mzCenterFun Chromatographic peak detection using the centWave method
mzCenterFun-method Chromatographic peak detection using the centWave method
mzCenterFun-method Chromatographic peak detection using the massifquant method
mzCenterFun<- Chromatographic peak detection using the centWave method
mzCenterFun<--method Chromatographic peak detection using the centWave method
mzCenterFun<--method Chromatographic peak detection using the massifquant method
MzClustParam High resolution peak grouping for single spectra samples
MzClustParam-class High resolution peak grouping for single spectra samples
mzdiff Chromatographic peak detection using the centWave method
mzdiff-method Chromatographic peak detection using the centWave method
mzdiff-method Chromatographic peak detection using the massifquant method
mzdiff-method Peak detection in the chromatographic time domain
mzdiff<- Chromatographic peak detection using the centWave method
mzdiff<--method Chromatographic peak detection using the centWave method
mzdiff<--method Chromatographic peak detection using the massifquant method
mzdiff<--method Peak detection in the chromatographic time domain
mzIntervalExtension Two-step centWave peak detection considering also isotopes
mzIntervalExtension-method Two-step centWave peak detection considering also isotopes
mzIntervalExtension<- Two-step centWave peak detection considering also isotopes
mzIntervalExtension<--method Two-step centWave peak detection considering also isotopes
mzrange Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzrange-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzVsRtBalance Peak grouping based on proximity in the mz-rt space
mzVsRtBalance-method Peak grouping based on proximity in the mz-rt space
mzVsRtBalance<- Peak grouping based on proximity in the mz-rt space
mzVsRtBalance<--method Peak grouping based on proximity in the mz-rt space

-- N --

nearbyPeak Single-spectrum non-chromatography MS data peak detection
nearbyPeak-method Single-spectrum non-chromatography MS data peak detection
nearbyPeak<- Single-spectrum non-chromatography MS data peak detection
nearbyPeak<--method Single-spectrum non-chromatography MS data peak detection
NearestPeaksParam Peak grouping based on proximity in the mz-rt space
NearestPeaksParam-class Peak grouping based on proximity in the mz-rt space
noise Chromatographic peak detection using the centWave method
noise-method Chromatographic peak detection using the centWave method
noise-method Chromatographic peak detection using the massifquant method
noise<- Chromatographic peak detection using the centWave method
noise<--method Chromatographic peak detection using the centWave method
noise<--method Chromatographic peak detection using the massifquant method
normalize-method XCMSnExp data manipulation methods inherited from MSnbase

-- O --

ObiwarpParam Align retention times across samples using Obiwarp
ObiwarpParam-class Align retention times across samples using Obiwarp

-- P --

PeakDensityParam Peak grouping based on time dimension peak densities
PeakDensityParam-class Peak grouping based on time dimension peak densities
peakGroupsMatrix Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix-method Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix<- Retention time correction based on alignment of house keeping peak groups
peakGroupsMatrix<--method Retention time correction based on alignment of house keeping peak groups
PeakGroupsParam Retention time correction based on alignment of house keeping peak groups
PeakGroupsParam-class Retention time correction based on alignment of house keeping peak groups
peakPlots-method Plot a grid of a large number of peaks
peakPlots-methods Plot a grid of a large number of peaks
peaks Class xcmsSet, a class for preprocessing peak data
peaks-method Class xcmsSet, a class for preprocessing peak data
peaks<- Class xcmsSet, a class for preprocessing peak data
peaks<--method Class xcmsSet, a class for preprocessing peak data
peakScaleRange Single-spectrum non-chromatography MS data peak detection
peakScaleRange-method Single-spectrum non-chromatography MS data peak detection
peakScaleRange<- Single-spectrum non-chromatography MS data peak detection
peakScaleRange<--method Single-spectrum non-chromatography MS data peak detection
peakTable Create report of aligned peak intensities
peakTable-method Create report of aligned peak intensities
peakThr Single-spectrum non-chromatography MS data peak detection
peakThr-method Single-spectrum non-chromatography MS data peak detection
peakThr<- Single-spectrum non-chromatography MS data peak detection
peakThr<--method Single-spectrum non-chromatography MS data peak detection
peakwidth Chromatographic peak detection using the centWave method
peakwidth-method Chromatographic peak detection using the centWave method
peakwidth-method Chromatographic peak detection using the massifquant method
peakwidth<- Chromatographic peak detection using the centWave method
peakwidth<--method Chromatographic peak detection using the centWave method
peakwidth<--method Chromatographic peak detection using the massifquant method
phenoData Class xcmsSet, a class for preprocessing peak data
phenoData-method Class xcmsSet, a class for preprocessing peak data
phenoData<- Class xcmsSet, a class for preprocessing peak data
phenoData<--method Class xcmsSet, a class for preprocessing peak data
pickPeaks-method XCMSnExp data manipulation methods inherited from MSnbase
plot, plot-methods Plot extracted ion chromatograms from multiple files
plot.xcmsEIC Plot extracted ion chromatograms from multiple files
plotAdjustedRtime Visualization of alignment results
plotChrom Plot extracted ion chromatograms from the profile matrix
plotChrom-method Plot extracted ion chromatograms from the profile matrix
plotEIC Plot extracted ion chromatograms for specified m/z range
plotEIC-method Plot extracted ion chromatograms for specified m/z range
plotPeaks Plot a grid of a large number of peaks
plotPeaks-method Plot a grid of a large number of peaks
plotQC Plot m/z and RT deviations for QC purposes without external reference data
plotRaw Scatterplot of raw data points
plotRaw-method Scatterplot of raw data points
plotrt Plot retention time deviation profiles
plotrt-method Plot retention time deviation profiles
plotScan Plot a single mass scan
plotScan-method Plot a single mass scan
plotSpec Plot mass spectra from the profile matrix
plotSpec-method Plot mass spectra from the profile matrix
plotSurf Plot profile matrix 3D surface using OpenGL
plotSurf-method Plot profile matrix 3D surface using OpenGL
plotTIC Plot total ion count
plotTIC-method Plot total ion count
plotTree Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
plotTree-method Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
polarity-method Two-step centWave peak detection considering also isotopes
polarity<- Two-step centWave peak detection considering also isotopes
polarity<--method Two-step centWave peak detection considering also isotopes
ppm Chromatographic peak detection using the centWave method
ppm-method Integrate areas of missing peaks
ppm-method Chromatographic peak detection using the centWave method
ppm-method Chromatographic peak detection using the massifquant method
ppm-method High resolution peak grouping for single spectra samples
ppm<- Chromatographic peak detection using the centWave method
ppm<--method Integrate areas of missing peaks
ppm<--method Chromatographic peak detection using the centWave method
ppm<--method Chromatographic peak detection using the massifquant method
ppm<--method High resolution peak grouping for single spectra samples
precursorMz-method Representation of chromatographic MS data
prefilter Chromatographic peak detection using the centWave method
prefilter-method Chromatographic peak detection using the centWave method
prefilter-method Chromatographic peak detection using the massifquant method
prefilter<- Chromatographic peak detection using the centWave method
prefilter<--method Chromatographic peak detection using the centWave method
prefilter<--method Chromatographic peak detection using the massifquant method
present Determine which peaks are absent / present in a sample class
present-method Determine which peaks are absent / present in a sample class
processDate Tracking data processing
processDate-method Tracking data processing
ProcessHistory Tracking data processing
processHistory Data container storing xcms preprocessing results
ProcessHistory-class Tracking data processing
processHistory-method Data container storing xcms preprocessing results
processHistoryTypes Data container storing xcms preprocessing results
processInfo Tracking data processing
processInfo-method Tracking data processing
processParam Tracking data processing
processParam-method Tracking data processing
processType Tracking data processing
processType-method Tracking data processing
productMz Representation of chromatographic MS data
productMz-method Representation of chromatographic MS data
profile-matrix The profile matrix
profinfo Class xcmsSet, a class for preprocessing peak data
profinfo-method Class xcmsRaw, a class for handling raw data
profinfo-method Class xcmsSet, a class for preprocessing peak data
profinfo<- Class xcmsSet, a class for preprocessing peak data
profinfo<--method Class xcmsSet, a class for preprocessing peak data
profMat The profile matrix
profMat-method Data container storing xcms preprocessing results
profMat-method The profile matrix
profMat-xcmsSet The profile matrix
profMedFilt Median filtering of the profile matrix
profMedFilt-method Median filtering of the profile matrix
profMethod Get and set method for generating profile data
profMethod-method Get and set method for generating profile data
profMethod-method Class xcmsSet, a class for preprocessing peak data
profMethod<- Get and set method for generating profile data
profMethod<--method Get and set method for generating profile data
profMz Class xcmsRaw, a class for handling raw data
profMz-method Class xcmsRaw, a class for handling raw data
profRange Specify a subset of profile mode data
profRange-method Specify a subset of profile mode data
profStep Get and set m/z step for generating profile data
profStep-method Get and set m/z step for generating profile data
profStep-method Class xcmsSet, a class for preprocessing peak data
profStep<- Get and set m/z step for generating profile data
profStep<--method Get and set m/z step for generating profile data
progressCallback Class xcmsSet, a class for preprocessing peak data
progressCallback-method Class xcmsSet, a class for preprocessing peak data
progressCallback<- Class xcmsSet, a class for preprocessing peak data
progressCallback<--method Class xcmsSet, a class for preprocessing peak data

-- R --

rawEIC Get extracted ion chromatograms for specified m/z range
rawEIC-method Get extracted ion chromatograms for specified m/z range
rawMat Get a raw data matrix
rawMat-method Get a raw data matrix
rawMat-methods Get a raw data matrix
removePeaks-method XCMSnExp data manipulation methods inherited from MSnbase
response Align retention times across samples using Obiwarp
response-method Align retention times across samples using Obiwarp
response<- Align retention times across samples using Obiwarp
response<--method Align retention times across samples using Obiwarp
retcor Correct retention time from different samples
retcor-method Correct retention time from different samples
retcor-methods Correct retention time from different samples
retcor.linear Align retention times across samples
retcor.linear-method Align retention times across samples
retcor.loess Align retention times across samples
retcor.loess-method Align retention times across samples
retcor.obiwarp Align retention times across samples with Obiwarp
retcor.obiwarp-method Align retention times across samples with Obiwarp
retcor.peakgroups Align retention times across samples
retcor.peakgroups-method Align retention times across samples
retexp Set retention time window to a specified width
revMz Class xcmsRaw, a class for handling raw data
revMz-method Class xcmsRaw, a class for handling raw data
ridgeLength Single-spectrum non-chromatography MS data peak detection
ridgeLength-method Single-spectrum non-chromatography MS data peak detection
ridgeLength<- Single-spectrum non-chromatography MS data peak detection
ridgeLength<--method Single-spectrum non-chromatography MS data peak detection
roiList Chromatographic peak detection using the centWave method
roiList-method Chromatographic peak detection using the centWave method
roiList<- Chromatographic peak detection using the centWave method
roiList<--method Chromatographic peak detection using the centWave method
roiScales Chromatographic peak detection using the centWave method
roiScales-method Chromatographic peak detection using the centWave method
roiScales<- Chromatographic peak detection using the centWave method
roiScales<--method Chromatographic peak detection using the centWave method
rtime-method Representation of chromatographic MS data
rtime-method Data container storing xcms preprocessing results
rtrange Class xcmsEIC, a class for multi-sample extracted ion chromatograms
rtrange-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms

-- S --

sampclass Class xcmsSet, a class for preprocessing peak data
sampclass-method Class xcmsSet, a class for preprocessing peak data
sampclass<- Class xcmsSet, a class for preprocessing peak data
sampclass<--method Class xcmsSet, a class for preprocessing peak data
sampleGroups Peak grouping based on time dimension peak densities
sampleGroups-method Peak grouping based on time dimension peak densities
sampleGroups-method High resolution peak grouping for single spectra samples
sampleGroups-method Peak grouping based on proximity in the mz-rt space
sampleGroups<- Peak grouping based on time dimension peak densities
sampleGroups<--method Peak grouping based on time dimension peak densities
sampleGroups<--method High resolution peak grouping for single spectra samples
sampleGroups<--method Peak grouping based on proximity in the mz-rt space
sampnames Get sample names
sampnames-method Get sample names
sampnames<- Class xcmsSet, a class for preprocessing peak data
sampnames<--method Class xcmsSet, a class for preprocessing peak data
scales Single-spectrum non-chromatography MS data peak detection
scales-method Single-spectrum non-chromatography MS data peak detection
scales<- Single-spectrum non-chromatography MS data peak detection
scales<--method Single-spectrum non-chromatography MS data peak detection
scanrange Class xcmsSet, a class for preprocessing peak data
scanrange-method Class xcmsRaw, a class for handling raw data
scanrange-method Class xcmsSet, a class for preprocessing peak data
setAs Data container storing xcms preprocessing results
show-method Representation of chromatographic MS data
show-method Generic parameter class
show-method Tracking data processing
show-method Data container storing xcms preprocessing results
show-method Align retention times across samples using Obiwarp
show-method Retention time correction based on alignment of house keeping peak groups
show-method Integrate areas of missing peaks
show-method Chromatographic peak detection using the centWave method
show-method Two-step centWave peak detection considering also isotopes
show-method Chromatographic peak detection using the massifquant method
show-method Peak detection in the chromatographic time domain
show-method Single-spectrum non-chromatography MS data peak detection
show-method Peak grouping based on time dimension peak densities
show-method High resolution peak grouping for single spectra samples
show-method Peak grouping based on proximity in the mz-rt space
show-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms
show-method Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
show-method A matrix of peaks
show-method Class xcmsRaw, a class for handling raw data
show-method Class xcmsSet, a class for preprocessing peak data
showError Extract processing errors
showError-method Extract processing errors
sigma Peak detection in the chromatographic time domain
sigma-method Peak detection in the chromatographic time domain
sigma<- Peak detection in the chromatographic time domain
sigma<--method Peak detection in the chromatographic time domain
smooth Retention time correction based on alignment of house keeping peak groups
smooth-method XCMSnExp data manipulation methods inherited from MSnbase
smooth-method Retention time correction based on alignment of house keeping peak groups
smooth<- Retention time correction based on alignment of house keeping peak groups
smooth<--method Retention time correction based on alignment of house keeping peak groups
snthresh Chromatographic peak detection using the centWave method
snthresh-method Chromatographic peak detection using the centWave method
snthresh-method Chromatographic peak detection using the massifquant method
snthresh-method Peak detection in the chromatographic time domain
snthresh-method Single-spectrum non-chromatography MS data peak detection
snthresh<- Chromatographic peak detection using the centWave method
snthresh<--method Chromatographic peak detection using the centWave method
snthresh<--method Chromatographic peak detection using the massifquant method
snthresh<--method Peak detection in the chromatographic time domain
snthresh<--method Single-spectrum non-chromatography MS data peak detection
snthreshIsoROIs Two-step centWave peak detection considering also isotopes
snthreshIsoROIs-method Two-step centWave peak detection considering also isotopes
snthreshIsoROIs<- Two-step centWave peak detection considering also isotopes
snthreshIsoROIs<--method Two-step centWave peak detection considering also isotopes
sortMz Class xcmsRaw, a class for handling raw data
sortMz-method Class xcmsRaw, a class for handling raw data
span Retention time correction based on alignment of house keeping peak groups
span-method Retention time correction based on alignment of house keeping peak groups
span<- Retention time correction based on alignment of house keeping peak groups
span<--method Retention time correction based on alignment of house keeping peak groups
specDist Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-method Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-methods Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist.cosine a Distance function based on matching peaks
specDist.cosine-method a Distance function based on matching peaks
specDist.meanMZmatch a Distance function based on matching peaks
specDist.meanMZmatch-method a Distance function based on matching peaks
specDist.peakCount a Distance function based on matching peaks
specDist.peakCount-method a Distance function based on matching peaks
specDist.peakCount-methods a Distance function based on matching peaks
specNoise Calculate noise for a sparse continuum mass spectrum
specPeaks Identify peaks in a sparse continuum mode spectrum
spectra-method Data container storing xcms preprocessing results
split, split-methods Divide an xcmsSet object
split.xcmsRaw Divide an xcmsRaw object
split.xcmsSet Divide an xcmsSet object
SSgauss Gaussian Model
steps Peak detection in the chromatographic time domain
steps-method Peak detection in the chromatographic time domain
steps<- Peak detection in the chromatographic time domain
steps<--method Peak detection in the chromatographic time domain
stitch Correct gaps in data
stitch-method Correct gaps in data
stitch-methods Correct gaps in data
stitch.netCDF Correct gaps in data
stitch.xml Correct gaps in data
subset-xcmsRaw Subset an xcmsRaw object by scans

-- T --

tuneIn Single-spectrum non-chromatography MS data peak detection
tuneIn-method Single-spectrum non-chromatography MS data peak detection
tuneIn<- Single-spectrum non-chromatography MS data peak detection
tuneIn<--method Single-spectrum non-chromatography MS data peak detection

-- U --

unions Chromatographic peak detection using the massifquant method
unions-method Chromatographic peak detection using the massifquant method
unions<- Chromatographic peak detection using the massifquant method
unions<--method Chromatographic peak detection using the massifquant method
updateObject-method Update an 'xcmsSet' object
useOriginalCode Enable usage of old xcms code

-- V --

verboseColumns Chromatographic peak detection using the centWave method
verboseColumns-method Chromatographic peak detection using the centWave method
verboseColumns-method Chromatographic peak detection using the massifquant method
verboseColumns-method Single-spectrum non-chromatography MS data peak detection
verboseColumns<- Chromatographic peak detection using the centWave method
verboseColumns<--method Chromatographic peak detection using the centWave method
verboseColumns<--method Chromatographic peak detection using the massifquant method
verboseColumns<--method Single-spectrum non-chromatography MS data peak detection
verify.mzQuantML Verify an mzQuantML file

-- W --

withWave Chromatographic peak detection using the massifquant method
withWave-method Chromatographic peak detection using the massifquant method
withWave<- Chromatographic peak detection using the massifquant method
withWave<--method Chromatographic peak detection using the massifquant method
write.cdf Save an xcmsRaw object to file
write.cdf-method Save an xcmsRaw object to file
write.mzdata Save an xcmsRaw object to a file
write.mzdata-method Save an xcmsRaw object to a file
write.mzQuantML Save an xcmsSet object to an PSI mzQuantML file
write.mzQuantML-method Save an xcmsSet object to an PSI mzQuantML file
writeMzTab Save a grouped xcmsSet object in mzTab-1.1 format file

-- X --

xcms-deprecated Deprecated functions in package 'xcms'
xcmsEIC-class Class xcmsEIC, a class for multi-sample extracted ion chromatograms
xcmsFileSource-class Base class for loading raw data from a file
xcmsFragments Constructor for xcmsFragments objects which holds Tandem MS peaks
xcmsFragments-class Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
XCMSnExp Data container storing xcms preprocessing results
XCMSnExp-class Data container storing xcms preprocessing results
XCMSnExp-filter XCMSnExp filtering and subsetting
xcmsPapply _Deprecated_: xcmsPapply
xcmsPeaks-class A matrix of peaks
xcmsRaw Constructor for xcmsRaw objects which reads NetCDF/mzXML files
xcmsRaw-class Class xcmsRaw, a class for handling raw data
xcmsSet Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files
xcmsSet-class Class xcmsSet, a class for preprocessing peak data
xcmsSource Create an 'xcmsSource' object in a flexible way
xcmsSource-class Virtual class for raw data sources
xcmsSource-method Base class for loading raw data from a file
xcmsSource-method Create an 'xcmsSource' object in a flexible way
xcmsSource-methods Create an 'xcmsSource' object in a flexible way
XProcessHistory Tracking data processing
XProcessHistory-class Tracking data processing

-- misc --

$-method Class xcmsSet, a class for preprocessing peak data
$<--method Class xcmsSet, a class for preprocessing peak data
[-method XCMSnExp data manipulation methods inherited from MSnbase
[-method Subset an xcmsRaw object by scans
[-method Class xcmsSet, a class for preprocessing peak data