Package index

All functions

AutoLockMass AutoLockMass-methods AutoLockMass,xcmsRaw-method

Automatic parameter for Lock mass fixing AutoLockMass ~~

BlankFlag() filterFeatures(<XcmsResult>,<BlankFlag>) filterFeatures(<SummarizedExperiment>,<BlankFlag>)

Flag features based on the intensity in blank samples

DratioFilter() filterFeatures(<XcmsResult>,<DratioFilter>) filterFeatures(<SummarizedExperiment>,<DratioFilter>)

Filter features based on the dispersion ratio

GenericParam()

Generic parameter class

adjustRtime(<XcmsExperiment>,<LamaParama>) matchLamasChromPeaks() summarizeLamaMatch() matchedRtimes() LamaParama() plot(<LamaParama>,<ANY>)

Landmark-based alignment: aligning a dataset against an external reference

PercentMissingFilter() filterFeatures(<XcmsResult>,<PercentMissingFilter>) filterFeatures(<SummarizedExperiment>,<PercentMissingFilter>)

Filter features based on the percentage of missing data

processParam(<XProcessHistory>) msLevel(<XProcessHistory>) processType(<ProcessHistory>) processDate(<ProcessHistory>) processInfo(<ProcessHistory>) fileIndex(<ProcessHistory>)

Tracking data processing

RsdFilter() filterFeatures(<XcmsResult>,<RsdFilter>) filterFeatures(<SummarizedExperiment>,<RsdFilter>)

Filter features based on their coefficient of variation

SSgauss()

Gaussian Model

processHistoryTypes() hasFilledChromPeaks(<XCMSnExp>) profMat(<OnDiskMSnExp>) hasAdjustedRtime(<XCMSnExp>) hasFeatures(<XCMSnExp>) hasChromPeaks(<XCMSnExp>) adjustedRtime(<XCMSnExp>) `adjustedRtime<-`(<XCMSnExp>) featureDefinitions(<XCMSnExp>) `featureDefinitions<-`(<XCMSnExp>) chromPeaks(<XCMSnExp>) `chromPeaks<-`(<XCMSnExp>) rtime(<XCMSnExp>) mz(<XCMSnExp>) intensity(<XCMSnExp>) spectra(<XCMSnExp>) processHistory(<XCMSnExp>) dropChromPeaks(<XCMSnExp>) dropFeatureDefinitions(<XCMSnExp>) dropAdjustedRtime(<XCMSnExp>) profMat(<XCMSnExp>) findChromPeaks(<XCMSnExp>,<Param>) dropFilledChromPeaks(<XCMSnExp>) spectrapply(<XCMSnExp>) c(<XCMSnExp>) chromPeakData(<XCMSnExp>) `chromPeakData<-`(<XCMSnExp>) plot(<XCMSnExp>,<missing>)

Data container storing xcms preprocessing results

`[`(<XCMSnExp>,<ANY>,<ANY>,<ANY>) `[[`(<XCMSnExp>,<ANY>,<ANY>) filterMsLevel(<XCMSnExp>) filterFile(<XCMSnExp>) filterMz(<XCMSnExp>) filterRt(<XCMSnExp>) split(<XCMSnExp>,<ANY>) filterChromPeaks(<XCMSnExp>) filterFeatureDefinitions(<XCMSnExp>)

XCMSnExp filtering and subsetting

bin(<XCMSnExp>) clean(<XCMSnExp>) filterAcquisitionNum(<XCMSnExp>) normalize(<XCMSnExp>) pickPeaks(<XCMSnExp>) removePeaks(<XCMSnExp>) smooth(<XCMSnExp>)

XCMSnExp data manipulation methods inherited from MSnbase

quantify(<XCMSnExp>) featureValues(<XCMSnExp>)

Accessing mz-rt feature data values

XChromatograms() XChromatogram() chromPeaks(<XChromatogram>) `chromPeaks<-`(<XChromatogram>) plot(<XChromatogram>,<ANY>) filterMz(<XChromatogram>) filterRt(<XChromatogram>) hasChromPeaks(<XChromatogram>) dropFilledChromPeaks(<XChromatogram>) chromPeakData(<XChromatogram>) `chromPeakData<-`(<XChromatogram>) refineChromPeaks(<XChromatogram>,<MergeNeighboringPeaksParam>) filterChromPeaks(<XChromatogram>) transformIntensity(<XChromatogram>) hasChromPeaks(<XChromatograms>) hasFilledChromPeaks(<XChromatograms>) chromPeaks(<XChromatograms>) chromPeakData(<XChromatograms>) filterMz(<XChromatograms>) filterRt(<XChromatograms>) plot(<XChromatograms>,<ANY>) processHistory(<XChromatograms>) hasFeatures(<XChromatograms>) dropFeatureDefinitions(<XChromatograms>) groupChromPeaks(<XChromatograms>,<PeakDensityParam>) featureDefinitions(<XChromatograms>) `[`(<XChromatograms>,<ANY>,<ANY>,<ANY>) featureValues(<XChromatograms>) plotChromPeakDensity(<XChromatograms>) dropFilledChromPeaks(<XChromatograms>) refineChromPeaks(<XChromatograms>,<MergeNeighboringPeaksParam>) filterChromPeaks(<XChromatograms>) transformIntensity(<XChromatograms>)

Containers for chromatographic and peak detection data

filterFeatureDefinitions() filterRt(<MsExperiment>) filterMzRange(<MsExperiment>) filterMz(<MsExperiment>) filterMsLevel(<MsExperiment>) uniqueMsLevels(<MsExperiment>) filterFile(<MsExperiment>) rtime(<MsExperiment>) fromFile(<MsExperiment>) fileNames(<MsExperiment>) polarity(<MsExperiment>) filterIsolationWindow(<MsExperiment>) chromatogram(<MsExperiment>) plot(<MsExperiment>,<missing>) c(<XcmsExperiment>) `[`(<XcmsExperiment>,<ANY>,<ANY>,<ANY>) filterIsolationWindow(<XcmsExperiment>) filterRt(<XcmsExperiment>) filterMzRange(<XcmsExperiment>) filterMsLevel(<XcmsExperiment>) hasChromPeaks(<XcmsExperiment>) dropChromPeaks(<XcmsExperiment>) `chromPeaks<-`(<XcmsExperiment>) chromPeaks(<XcmsExperiment>) `chromPeakData<-`(<XcmsExperiment>) chromPeakData(<XcmsExperiment>) filterChromPeaks(<XcmsExperiment>) dropAdjustedRtime(<XcmsExperiment>) hasAdjustedRtime(<MsExperiment>) rtime(<XcmsExperiment>) adjustedRtime(<XcmsExperiment>) hasFeatures(<XcmsExperiment>) featureArea(<XcmsResult>) `featureDefinitions<-`(<XcmsExperiment>) featureDefinitions(<XcmsExperiment>) dropFeatureDefinitions(<XcmsExperiment>) hasFilledChromPeaks(<XcmsExperiment>) dropFilledChromPeaks(<XcmsExperiment>) quantify(<XcmsExperiment>) featureValues(<XcmsExperiment>) chromatogram(<XcmsExperiment>) processHistory(<XcmsExperiment>) filterFile(<XcmsExperiment>)

Next Generation xcms Result Object

toXcmsExperimentHdf5() toXcmsExperiment() chromPeakData(<XcmsExperimentHdf5>) filterChromPeaks(<XcmsExperimentHdf5>) adjustRtimePeakGroups(<XcmsExperimentHdf5>,<PeakGroupsParam>) filterFeatureDefinitions(<XcmsExperimentHdf5>)

xcms result object for very large data sets

absent absent,xcmsSet-method present present,xcmsSet-method

Determine which peaks are absent / present in a sample class

adjustRtime() adjustRtimePeakGroups() PeakGroupsParam() ObiwarpParam() `binSize<-`(<ObiwarpParam>)

Alignment: Retention time correction methods.

applyAdjustedRtime()

Replace raw with adjusted retention times

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

c.xcmsSet c, c-methods

Combine xcmsSet objects

CalibrantMassParam() isCalibrated() calibrate(<XCMSnExp>)

Calibrant mass based calibration of chromatgraphic peaks

calibrate calibrate,xcmsSet-method

Calibrate peaks for correcting unprecise m/z values

chromPeakChromatograms()

Extract an ion chromatogram for each chromatographic peak

chromPeakSpectra()

Extract spectra associated with chromatographic peaks

chromPeakSummary() BetaDistributionParam()

Chromatographic peak summaries

chromatogram(<XCMSnExp>)

Extracting chromatograms

collect-methods collect collect,xcmsRaw-method collect,xcmsFragments-method

Collect MS^n peaks into xcmsFragments

correlate(<Chromatogram>,<Chromatogram>) correlate(<MChromatograms>,<missing>) correlate(<MChromatograms>,<MChromatograms>)

Correlate chromatograms

diffreport diffreport,xcmsSet-method

Create report of analyte differences

dirname(<OnDiskMSnExp>) `dirname<-`(<OnDiskMSnExp>)

Change the file path of an OnDiskMSnExp object

do_adjustRtime_peakGroups()

Align spectrum retention times across samples using peak groups found in most samples

do_findChromPeaks_centWave()

Core API function for centWave peak detection

do_findChromPeaks_centWaveWithPredIsoROIs() do_findChromPeaks_addPredIsoROIs()

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

estimatePrecursorIntensity(<MsExperiment>) estimatePrecursorIntensity(<OnDiskMSnExp>)

Estimate precursor intensity for MS level 2 spectra

etg()

Empirically Transformed Gaussian function

exportMetaboAnalyst()

Export data for use in MetaboAnalyst

extractMsData(<OnDiskMSnExp>) extractMsData(<XCMSnExp>)

DEPRECATED: Extract a data.frame containing MS data

featureGroups(<XcmsResult>) `featureGroups<-`(<XcmsResult>)

Compounding of LC-MS features

featureChromatograms()

Extract ion chromatograms for each feature

featureSpectra()

Extract spectra associated with features

featureSummary()

Simple feature summaries

fillChromPeaks() FillChromPeaksParam() ChromPeakAreaParam()

Gap Filling

fillPeaks fillPeaks,xcmsSet-method

Integrate areas of missing peaks

fillPeaks.MSW fillPeaks.MSW,xcmsSet-method

Integrate areas of missing peaks in FTICR-MS data

fillPeaks.chrom fillPeaks.chrom,xcmsSet-method

Integrate areas of missing peaks

filterColumnsIntensityAbove(<MChromatograms>) filterColumnsKeepTop(<MChromatograms>) filterColumnsIntensityAbove(<XChromatograms>) filterColumnsKeepTop(<XChromatograms>)

Filtering sets of chromatographic data

filterFeatures

Filtering of features based on conventional quality assessment

findChromPeaks(<Chromatogram>,<CentWaveParam>) findChromPeaks(<MChromatograms>,<CentWaveParam>) findChromPeaks(<MChromatograms>,<MatchedFilterParam>)

centWave-based peak detection in purely chromatographic data

findChromPeaks(<Chromatogram>,<MatchedFilterParam>)

matchedFilter-based peak detection in purely chromatographic data

CentWaveParam() findChromPeaks(<OnDiskMSnExp>,<CentWaveParam>) as.list(<CentWaveParam>)

Chromatographic peak detection using the centWave method

CentWavePredIsoParam() findChromPeaks(<OnDiskMSnExp>,<CentWavePredIsoParam>)

Two-step centWave peak detection considering also isotopes

MassifquantParam() findChromPeaks(<OnDiskMSnExp>,<MassifquantParam>)

Chromatographic peak detection using the massifquant method

MatchedFilterParam() findChromPeaks(<OnDiskMSnExp>,<MatchedFilterParam>)

Peak detection in the chromatographic time domain

findChromPeaks()

Chromatographic Peak Detection

findChromPeaksIsolationWindow()

Data independent acquisition (DIA): peak detection in isolation windows

findMZ()

Find fragment ions in xcmsFragment objects

MSWParam() findChromPeaks(<OnDiskMSnExp>,<MSWParam>)

Single-spectrum non-chromatography MS data peak detection

findPeaks-methods findPeaks findPeaks,xcmsRaw-method

Feature detection for GC/MS and LC/MS Data - methods

findPeaks.MS1 findPeaks.MS1,xcmsRaw-method

Collecting MS1 precursor peaks

findPeaks.MSW(<xcmsRaw>)

Peak detection for single-spectrum non-chromatography MS data

findPeaks.addPredictedIsotopeFeatures findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method

Feature detection based on predicted isotope features for high resolution LC/MS data

findPeaks.centWave findPeaks.centWave,xcmsRaw-method

Feature detection for high resolution LC/MS data

findPeaks.centWaveWithPredictedIsotopeROIs findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method

Feature detection with centWave and additional isotope features

findPeaks.massifquant findPeaks.massifquant,xcmsRaw-method

Feature detection for XC-MS data.

findPeaks.matchedFilter(<xcmsRaw>)

Peak detection in the chromatographic time domain

findneutral()

Find neutral losses in xcmsFragment objects

getEIC getEIC,xcmsRaw-method getEIC,xcmsSet-method

Get extracted ion chromatograms for specified m/z ranges

getPeaks getPeaks,xcmsRaw-method

Get peak intensities for specified regions

getScan getScan,xcmsRaw-method getMsnScan getMsnScan,xcmsRaw-method

Get m/z and intensity values for a single mass scan

getSpec getSpec,xcmsRaw-method

Get average m/z and intensity values for multiple mass scans

getXcmsRaw getXcmsRaw,xcmsSet-method

Load the raw data for one or more files in the xcmsSet

group-methods group group,xcmsSet-method

Group peaks from different samples together

group.density group.density,xcmsSet-method

Group peaks from different samples together

group.mzClust group.mzClust,xcmsSet-method

Group Peaks via High Resolution Alignment

group.nearest group.nearest,xcmsSet-method

Group peaks from different samples together

groupChromPeaks() PeakDensityParam() MzClustParam() NearestPeaksParam() as.list(<PeakDensityParam>)

Correspondence: group chromatographic peaks across samples

groupFeatures(<XcmsResult>,<AbundanceSimilarityParam>)

Compounding/feature grouping based on similarity of abundances across samples

EicSimilarityParam() groupFeatures(<XcmsResult>,<EicSimilarityParam>)

Compounding/feature grouping based on similarity of extracted ion chromatograms

groupFeatures(<XcmsResult>,<SimilarRtimeParam>)

Compounding/feature grouping based on similar retention times

groupOverlaps()

Group overlapping ranges

groupnames(<XCMSnExp>)

Generate unique group (feature) names based on mass and retention time

groupnames groupnames,xcmsEIC-method groupnames,xcmsSet-method

Generate unque names for peak groups

groupval groupval,xcmsSet-method

Extract a matrix of peak values for each group

highlightChromPeaks()

Add definition of chromatographic peaks to an extracted chromatogram plot

image,xcmsRaw-method

Plot log intensity image of a xcmsRaw object

imputeLinInterpol()

Impute values for empty elements in a vector using linear interpolation

imputeRowMin()

Replace missing values with a proportion of the row minimum

imputeRowMinRand()

Impute missing values with random numbers based on the row minimum

isolationWindowTargetMz(<OnDiskMSnExp>)

Extract isolation window target m/z definition

levelplot,xcmsRaw-method levelplot,xcmsSet-method

Plot log intensity image of a xcmsRaw object

loadRaw loadRaw-methods loadRaw,xcmsSource-method loadRaw,xcmsFileSource-method

Read binary data from a source

loadXcmsData()

LC-MS preprocessing result test data sets

manualChromPeaks() manualFeatures()

Manual peak integration and feature definition

medianFilter()

Apply a median filter to a matrix

msn2xcmsRaw()

Copy MSn data in an xcmsRaw to the MS slots

overlappingFeatures()

Identify overlapping features

peakPlots-methods peakPlots,xcmsSet-method

Plot a grid of a large number of peaks

peakTable peakTable,xcmsSet-method

Create report of aligned peak intensities

peaksWithCentWave()

Identify peaks in chromatographic data using centWave

peaksWithMatchedFilter()

Identify peaks in chromatographic data using matchedFilter

phenoDataFromPaths()

Derive experimental design from file paths

plot.xcmsEIC plot, plot-methods

Plot extracted ion chromatograms from multiple files

plotAdjustedRtime()

Visualization of Alignment Results

plotChrom plotChrom,xcmsRaw-method

Plot extracted ion chromatograms from the profile matrix

plotChromPeakDensity(<XCMSnExp>)

Plot chromatographic peak density along the retention time axis

plotChromPeaks() plotChromPeakImage()

General visualizations of peak detection results

plotChromatogramsOverlay(<MChromatograms>) plotChromatogramsOverlay(<XChromatograms>)

Plot multiple chromatograms into the same plot

plotEIC plotEIC,xcmsRaw-method

Plot extracted ion chromatograms for specified m/z range

plotFeatureGroups()

Plot feature groups in the m/z-retention time space

plotMsData()

DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D plot for one sample

plotPeaks plotPeaks,xcmsRaw-method

Plot a grid of a large number of peaks

plotPrecursorIons()

General visualization of precursor ions of LC-MS/MS data

plotQC()

Plot m/z and RT deviations for QC purposes without external reference data

plotRaw plotRaw,xcmsRaw-method

Scatterplot of raw data points

plotScan plotScan,xcmsRaw-method

Plot a single mass scan

plotSpec plotSpec,xcmsRaw-method

Plot mass spectra from the profile matrix

plotSurf plotSurf,xcmsRaw-method

Plot profile matrix 3D surface using OpenGL

plotTIC plotTIC,xcmsRaw-method

Plot total ion count

plotrt plotrt,xcmsSet-method

Plot retention time deviation profiles

profMat(<MsExperiment>) profMat(<xcmsRaw>)

The profile matrix

profMedFilt profMedFilt,xcmsRaw-method

Median filtering of the profile matrix

profMethod profMethod<- profMethod,xcmsRaw-method profMethod<-,xcmsRaw-method

Get and set method for generating profile data

profRange profRange,xcmsRaw-method

Specify a subset of profile mode data

profStep profStep<- profStep,xcmsRaw-method profStep<-,xcmsRaw-method

Get and set m/z step for generating profile data

rawEIC rawEIC,xcmsRaw-method

Get extracted ion chromatograms for specified m/z range

rawMat rawMat-methods rawMat,xcmsRaw-method

Get a raw data matrix

reconstructChromPeakSpectra()

Data independent acquisition (DIA): reconstruct MS2 spectra

refineChromPeaks() CleanPeaksParam() MergeNeighboringPeaksParam() FilterIntensityParam()

Refine Identified Chromatographic Peaks

removeIntensity(<Chromatogram>) removeIntensity(<MChromatograms>) removeIntensity(<XChromatogram>)

Remove intensities from chromatographic data

retcor-methods retcor retcor,xcmsSet-method

Correct retention time from different samples

retcor.obiwarp retcor.obiwarp,xcmsSet-method

Align retention times across samples with Obiwarp

retcor.peakgroups retcor.peakgroups,xcmsSet-method retcor.loess retcor.loess,xcmsSet-method retcor.linear retcor.linear,xcmsSet-method

Align retention times across samples

retexp()

Set retention time window to a specified width

rla() rowRla()

Calculate relative log abundances

sampnames sampnames,xcmsEIC-method sampnames,xcmsSet-method

Get sample names

showError(<xcmsSet>)

Extract processing errors

specDist-methods specDist specDist,xcmsSet-method

Distance methods for xcmsSet, xcmsRaw and xsAnnotate

specDist.cosine()

a Distance function based on matching peaks

specDist.meanMZmatch()

a Distance function based on matching peaks

specDist.peakCount()

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.xcmsRaw

Divide an xcmsRaw object

split.xcmsSet split, split-methods

Divide an xcmsSet object

stitch stitch-methods stitch,xcmsRaw-method stitch.netCDF stitch.xml makeacqNum makeacqNum, xcmsRaw-method

Correct gaps in data

`[`(<xcmsRaw>,<logicalOrNumeric>,<missing>,<missing>)

Subset an xcmsRaw object by scans

updateObject(<xcmsSet>)

Update an xcmsSet object

useOriginalCode()

Enable usage of old xcms code

verify.mzQuantML()

Verify an mzQuantML file

write.cdf write.cdf,xcmsRaw-method

Save an xcmsRaw object to file

write.mzQuantML write.mzQuantML,xcmsSet-method

Save an xcmsSet object to an PSI mzQuantML file

write.mzdata write.mzdata,xcmsRaw-method

Save an xcmsRaw object to a file

writeMSData(<XCMSnExp>,<character>)

Export MS data to mzML/mzXML files

writeMzTab

Save a grouped xcmsSet object in mzTab-1.1 format file

xcms-deprecated

Deprecated functions in package ‘xcms’

xcmsEIC-class mzrange,xcmsEIC-method mzrange rtrange,xcmsEIC-method rtrange

Class xcmsEIC, a class for multi-sample extracted ion chromatograms

xcmsFileSource-class xcmsSource,character-method

Base class for loading raw data from a file

xcmsFragments-class plotTree plotTree,xcmsFragments-method

Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data

xcmsFragments()

Constructor for xcmsFragments objects which holds Tandem MS peaks

xcmsPeaks-class

A matrix of peaks

xcmsRaw-class mslevel,xcmsRaw-method profinfo,xcmsRaw-method profMz,xcmsRaw-method profMz revMz,xcmsRaw-method revMz scanrange,xcmsRaw-method sortMz,xcmsRaw-method sortMz levelplot findmzROI findmzROI,xcmsRaw-method

Class xcmsRaw, a class for handling raw data

xcmsRaw() deepCopy()

Constructor for xcmsRaw objects which reads NetCDF/mzXML files

xcmsSet-class [,xcmsSet-method [,xcmsSet,ANY,ANY,ANY-method $<-,xcmsSet-method $,xcmsSet-method filepaths<-,xcmsSet-method filepaths<- filepaths,xcmsSet-method filepaths groupidx<-,xcmsSet-method groupidx<- groupidx,xcmsSet-method groupidx groups<-,xcmsSet-method groups<- groups,xcmsSet-method groups mslevel,xcmsSet-method mslevel peaks<-,xcmsSet-method peaks<- peaks,xcmsSet-method peaks phenoData phenoData,xcmsSet-method phenoData<- phenoData<-,xcmsSet-method phenoData<-,xcmsSet,ANY-method profinfo<-,xcmsSet-method profinfo<- profinfo,xcmsSet-method profinfo profMethod,xcmsSet-method profStep,xcmsSet-method progressCallback progressCallback,xcmsSet-method progressCallback<- progressCallback<-,xcmsSet-method sampclass<-,xcmsSet-method sampclass<- sampclass,xcmsSet-method sampclass sampnames<-,xcmsSet-method sampnames<- scanrange,xcmsSet-method scanrange

Class xcmsSet, a class for preprocessing peak data

xcmsSet()

Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files

xcmsSource-class

Virtual class for raw data sources

xcmsSource xcmsSource-methods xcmsSource,xcmsSource-method

Create an xcmsSource object in a flexible way