# LC/MS and GC/MS Data Analysis

## Documentation for package ‘xcms’ version 1.50.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G I L M P R S 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
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' ~~

## -- 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
collect | Collect MS^n peaks into xcmsFragments
collect-method | Collect MS^n peaks into xcmsFragments
collect-methods | Collect MS^n peaks into xcmsFragments

## -- 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

## -- E --

etg | Empirically Transformed Gaussian function

## -- F --

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
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
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.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 | Feature detection in the chromatographic time domain
findPeaks.matchedFilter-method | Feature detection in the chromatographic time domain
findPeaks.MS1 | Collecting MS1 precursor peaks
findPeaks.MS1-method | Collecting MS1 precursor peaks
findPeaks.MSW | Feature detection for single-spectrum non-chromatography MS data
findPeaks.MSW-method | Feature detection for single-spectrum non-chromatography MS data

## -- G --

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
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

## -- I --

image-method | Plot log intensity image of a xcmsRaw object

## -- L --

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

## -- M --

makeacqNum | Correct gaps in data
makeacqNum-method | Correct gaps in data
medianFilter | Apply a median filter to a matrix
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
mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms

## -- P --

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
peakTable | Create report of aligned peak intensities
peakTable-method | Create report of aligned peak intensities
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
plot, plot-methods | Plot extracted ion chromatograms from multiple files
plot.xcmsEIC | Plot extracted ion chromatograms from multiple files
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
present | Determine which peaks are absent / present in a sample class
present-method | Determine which peaks are absent / present in a sample class
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
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
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
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
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
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
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
sortMz | Class xcmsRaw, a class for handling raw data
sortMz-method | Class xcmsRaw, a class for handling raw data
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
split, split-methods | Divide an xcmsSet object
split.xcmsRaw | Divide an xcmsRaw object
split.xcmsSet | Divide an xcmsSet object
SSgauss | Gaussian Model
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

## -- U --

updateObject-method | Update an 'xcmsSet' object

## -- V --

valueCount2ScanIndex | Create index vector for internal C calls
verify.mzQuantML | Verify an mzQuantML file

## -- W --

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
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

## -- misc --

$-method | Class xcmsSet, a class for preprocessing peak data
$<--method | Class xcmsSet, a class for preprocessing peak data
[-method | Class xcmsSet, a class for preprocessing peak data