Man pages for xcms
LC-MS and GC-MS Data Analysis

absent-methodsDetermine which peaks are absent / present in a sample class
adjustRtimeAlignment: Retention time correction methods.
adjustRtime-obiwarpAlign retention times across samples using Obiwarp
adjustRtime-peakGroupsRetention time correction based on alignment of house keeping...
align-ChromatogramAligning chromatographic data
applyAdjustedRtimeReplace raw with adjusted retention times
AutoLockMass-methodsAutomatic parameter for Lock mass fixing 'AutoLockMass' ~~
binYonXAggregate values in y for bins defined on x
breaks_on_binSizeGenerate breaks for binning using a defined bin size.
breaks_on_nBinsGenerate breaks for binning
calibrateCalibrate peaks for correcting unprecise m/z values
calibrate-calibrant-massCalibrant mass based calibration of chromatgraphic peaks
chromatogram-methodExtracting chromatograms
chromatographic-peak-detectionChromatographic peak detection methods.
chromPeakSpectraExtract (MS2) spectra associated with chromatographic peaks
collect-methodsCollect MS^n peaks into xcmsFragments
colMaxFind row and column maximum values
correlate-ChromatogramCorrelate chromatograms
c.xcmsSetCombine xcmsSet objects
descendZeroFind start and end points of a peak
diffreport-methodsCreate report of analyte differences
dirnameChange the file path of an 'OnDiskMSnExp' object
do_adjustRtime_peakGroupsAlign spectrum retention times across samples using peak...
do_findChromPeaks_centWaveCore API function for centWave peak detection
do_findChromPeaks_centWaveWithPredIsoROIsCore API function for two-step centWave peak detection with...
do_findChromPeaks_massifquantCore API function for massifquant peak detection
do_findChromPeaks_matchedFilterCore API function for matchedFilter peak detection
do_findPeaks_MSWCore API function for single-spectrum non-chromatography MS...
do_groupChromPeaks_densityCore API function for peak density based chromatographic peak...
do_groupChromPeaks_nearestCore API function for chromatic peak grouping using a nearest...
do_groupPeaks_mzClustCore API function for peak grouping using mzClust
doubleMatrixAllocate double, integer, or logical matricies
estimatePrecursorIntensityEstimate precursor intensity for MS level 2 spectra
etgEmpirically Transformed Gaussian function
exportMetaboAnalystExport data for use in MetaboAnalyst
extractMsData-methodDEPRECATED: Extract a 'data.frame' containing MS data
featureChromatogramsExtract ion chromatograms for each feature
featureSpectraExtract (MS2) spectra associated with features
featureSummarySimple feature summaries
fillChromPeaksIntegrate areas of missing peaks
fillPeaks.chrom-methodsIntegrate areas of missing peaks
fillPeaks-methodsIntegrate areas of missing peaks
fillPeaks.MSW-methodsIntegrate areas of missing peaks in FTICR-MS data
filter-MChromatogramsFiltering sets of chromatographic data
filtfftApply an convolution filter using an FFT
findChromPeaks-centWaveChromatographic peak detection using the centWave method
findChromPeaks-centWaveWithPredIsoROIsTwo-step centWave peak detection considering also isotopes
findChromPeaks-Chromatogram-CentWaveParamcentWave-based peak detection in purely chromatographic data
findChromPeaks-Chromatogram-MatchedFiltermatchedFilter-based peak detection in purely chromatographic...
findChromPeaksIsolationWindowData independent acquisition (DIA): peak detection in...
findChromPeaks-massifquantChromatographic peak detection using the massifquant method
findChromPeaks-matchedFilterPeak detection in the chromatographic time domain
findEqualGreaterFind values in sorted vectors
findMZFind fragment ions in xcmsFragment objects
findneutralFind neutral losses in xcmsFragment objects
findPeaks.addPredictedIsotopeFeatures-methodsFeature detection based on predicted isotope features for...
findPeaks.centWave-methodsFeature detection for high resolution LC/MS data
findPeaks.centWaveWithPredictedIsotopeROIs-methodsFeature detection with centWave and additional isotope...
findPeaks.massifquant-methodsFeature detection for XC-MS data.
findPeaks.matchedFilter-xcmsRaw-methodPeak detection in the chromatographic time domain
findPeaks-methodsFeature detection for GC/MS and LC/MS Data - methods
findPeaks.MS1-methodsCollecting MS1 precursor peaks
findPeaks-MSWSingle-spectrum non-chromatography MS data peak detection
findPeaks.MSW-xcmsRaw-methodPeak detection for single-spectrum non-chromatography MS data
GenericParamGeneric parameter class
getEIC-methodsGet extracted ion chromatograms for specified m/z ranges
getPeaks-methodsGet peak intensities for specified regions
getScan-methodsGet m/z and intensity values for a single mass scan
getSpec-methodsGet average m/z and intensity values for multiple mass scans
getXcmsRaw-methodsLoad the raw data for one or more files in the xcmsSet
groupChromPeaksCorrespondence: Chromatographic peak grouping methods.
groupChromPeaks-densityPeak grouping based on time dimension peak densities
groupChromPeaks-mzClustHigh resolution peak grouping for single spectra samples
groupChromPeaks-nearestPeak grouping based on proximity in the mz-rt space
group.densityGroup peaks from different samples together
group-methodsGroup peaks from different samples together
group.mzClustGroup Peaks via High Resolution Alignment
groupnames-methodsGenerate unque names for peak groups
groupnames-XCMSnExpGenerate unique group (feature) names based on mass and...
group.nearestGroup peaks from different samples together
groupOverlapsGroup overlapping ranges
groupval-methodsExtract a matrix of peak values for each group
highlightChromPeaksAdd definition of chromatographic peaks to an extracted...
image.xcmsRawPlot log intensity image of a xcmsRaw object
imputeLinInterpolImpute values for empty elements in a vector using linear...
imputeRowMinReplace missing values with a proportion of the row minimum
imputeRowMinRandImpute missing values with random numbers based on the row...
isolationWindowTargetMz-OnDiskMSnExp-methodExtract isolation window target m/z definition
levelplot.xcmsRawPlot log intensity image of a xcmsRaw object
loadRaw-methodsRead binary data from a source
medianFilterApply a median filter to a matrix
msn2xcmsRawCopy MSn data in an xcmsRaw to the MS slots
na.flatfillFill in NA values at the extremes of a vector
normalize-ChromatogramNormalize chromatographic data
overlappingFeaturesIdentify overlapping features
panel.corCorrelation coefficient panel for pairs function
peakPlots-methodsPlot a grid of a large number of peaks
peaksWithCentWaveIdentify peaks in chromatographic data using centWave
peaksWithMatchedFilterIdentify peaks in chromatographic data using matchedFilter
peakTable-methodsCreate report of aligned peak intensities
phenoDataFromPathsDerive experimental design from file paths
plotAdjustedRtimeVisualization of alignment results
plotChrom-methodsPlot extracted ion chromatograms from the profile matrix
plotChromPeakDensityPlot chromatographic peak density along the retention time...
plotChromPeaksGeneral visualizations of peak detection results
plotEIC-methodsPlot extracted ion chromatograms for specified m/z range
plotMsDataDEPRECATED: Create a plot that combines a XIC and a mz/rt 2D...
plotPeaks-methodsPlot a grid of a large number of peaks
plotQCPlot m/z and RT deviations for QC purposes without external...
plotRaw-methodsScatterplot of raw data points
plotrt-methodsPlot retention time deviation profiles
plotScan-methodsPlot a single mass scan
plotSpec-methodsPlot mass spectra from the profile matrix
plotSurf-methodsPlot profile matrix 3D surface using OpenGL
plotTIC-methodsPlot total ion count
plot.xcmsEICPlot extracted ion chromatograms from multiple files
ProcessHistory-classTracking data processing
profGenerateGeneration of profile data
profMat-xcmsSetThe profile matrix
profMedFilt-methodsMedian filtering of the profile matrix
profMethod-methodsGet and set method for generating profile data
profRange-methodsSpecify a subset of profile mode data
profStep-methodsGet and set m/z step for generating profile data
pvalGenerate p-values for a vector of t-statistics
rawEIC-methodsGet extracted ion chromatograms for specified m/z range
rawMat-methodsGet a raw data matrix
reconstructChromPeakSpectraData independent acquisition (DIA): reconstruct MS2 spectra
rectUniqueDetermine a subset of rectangles with unique, non-overlapping...
refineChromPeaks-cleanRemove chromatographic peaks with too large rt width
refineChromPeaks-filter-intensityRemove chromatographic peaks based on intensity
refineChromPeaks-mergeMerge neighboring and overlapping chromatographic peaks
removeIntensity-ChromatogramRemove intensities from chromatographic data
retcor-methodsCorrect retention time from different samples
retcor.obiwarp-methodsAlign retention times across samples with Obiwarp
retcor.peakgroups-methodsAlign retention times across samples
retexpSet retention time window to a specified width
rlaCalculate relative log abundances 'rla' calculates the...
sampnames-methodsGet sample names
showError-xcmsSet-methodExtract processing errors
specDist.cosine-methodsa Distance function based on matching peaks
specDist.meanMZmatch-methodsa Distance function based on matching peaks
specDist-methodsDistance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist.peakCount-methodsa Distance function based on matching peaks
specNoiseCalculate noise for a sparse continuum mass spectrum
specPeaksIdentify peaks in a sparse continuum mode spectrum
split.xcmsRawDivide an xcmsRaw object
split.xcmsSetDivide an xcmsSet object
SSgaussGaussian Model
stitch-methodsCorrect gaps in data
sub-xcmsRaw-logicalOrNumeric-missing-missing-methodSubset an xcmsRaw object by scans
updateObject-xcmsSet-methodUpdate an 'xcmsSet' object
useOriginalCodeEnable usage of old xcms code
verify.mzQuantMLVerify an mzQuantML file
write.cdf-methodsSave an xcmsRaw object to file
writeMSData-XCMSnExp-character-methodExport MS data to mzML/mzXML files
write.mzdata-methodsSave an xcmsRaw object to a file
write.mzQuantMLSave an xcmsSet object to an PSI mzQuantML file
writeMzTabSave a grouped xcmsSet object in mzTab-1.1 format file
XChromatogramContainers for chromatographic and peak detection data
xcms-deprecatedDeprecated functions in package 'xcms'
xcmsEIC-classClass xcmsEIC, a class for multi-sample extracted ion...
xcmsFileSource-classBase class for loading raw data from a file
xcmsFragmentsConstructor for xcmsFragments objects which holds Tandem MS...
xcmsFragments-classClass xcmsFragments, a class for handling Tandem MS and...
XCMSnExp-classData container storing xcms preprocessing results
XCMSnExp-filter-methodsXCMSnExp filtering and subsetting
XCMSnExp-inherited-methodsXCMSnExp data manipulation methods inherited from MSnbase
XCMSnExp-peak-grouping-resultsAccessing mz-rt feature data values
xcmsPeaks-classA matrix of peaks
xcmsRawConstructor for xcmsRaw objects which reads NetCDF/mzXML...
xcmsRaw-classClass xcmsRaw, a class for handling raw data
xcmsSetConstructor for xcmsSet objects which finds peaks in...
xcmsSet-classClass xcmsSet, a class for preprocessing peak data
xcmsSource-classVirtual class for raw data sources
xcmsSource-methodsCreate an 'xcmsSource' object in a flexible way
xcms documentation built on Nov. 8, 2020, 5:13 p.m.