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

absent-methodsDetermine which peaks are absent / present in a sample class
adjustRtimeAlignment: Retention time correction methods.
applyAdjustedRtimeReplace raw with adjusted retention times
AutoLockMass-methodsAutomatic parameter for Lock mass fixing 'AutoLockMass' ~~
binYonXAggregate values in y for bins defined on x
BlankFlagFlag features based on the intensity in blank samples
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
chromPeakChromatogramsExtract an ion chromatogram for each chromatographic peak
chromPeakSpectraExtract 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
DratioFilterFilter features based on the dispersion ratio
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
feature-groupingCompounding of LC-MS features
featureSpectraExtract spectra associated with features
featureSummarySimple feature summaries
fillChromPeaksGap Filling
fillPeaks.chrom-methodsIntegrate areas of missing peaks
fillPeaks-methodsIntegrate areas of missing peaks
fillPeaks.MSW-methodsIntegrate areas of missing peaks in FTICR-MS data
filterFeaturesFiltering of features based on conventional quality...
filter-MChromatogramsFiltering sets of chromatographic data
filtfftApply an convolution filter using an FFT
findChromPeaksChromatographic Peak Detection
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: group chromatographic peaks across samples
group.densityGroup peaks from different samples together
groupFeatures-abundance-correlationCompounding/feature grouping based on similarity of...
groupFeatures-eic-similarityCompounding/feature grouping based on similarity of extracted...
groupFeatures-similar-rtimeCompounding/feature grouping based on similar retention times
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
LamaParamaLandmark-based alignment: aligning a dataset against an...
levelplot.xcmsRawPlot log intensity image of a xcmsRaw object
loadRaw-methodsRead binary data from a source
loadXcmsDataLC-MS preprocessing result test data sets
manualChromPeaksManual peak integration and feature definition
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
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
PercentMissingFilterFilter features based on the percentage of missing data
phenoDataFromPathsDerive experimental design from file paths
PlainTextParamStore contents of 'MsExperiment' and 'XcmsExperiment' objects...
plotAdjustedRtimeVisualization of Alignment Results
plotChromatogramsOverlayPlot multiple chromatograms into the same plot
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
plotFeatureGroupsPlot feature groups in the m/z-retention time space
plotMsDataDEPRECATED: Create a plot that combines a XIC and a mz/rt 2D...
plotPeaks-methodsPlot a grid of a large number of peaks
plotPrecursorIonsGeneral visualization of precursor ions of LC-MS/MS data
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
RDataParamStore 'XcmsExperiment' object as .RData file
reconstructChromPeakSpectraData independent acquisition (DIA): reconstruct MS2 spectra
rectUniqueDetermine a subset of rectangles with unique, non-overlapping...
refineChromPeaksRefine Identified 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
RsdFilterFilter features based on their coefficient of variation
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
storeResultsSave xcms result objects in a specified format
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...
XcmsExperimentNext Generation 'xcms' Result Object
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
sneumann/xcms documentation built on June 5, 2024, 4:28 p.m.