xcms: LC/MS and GC/MS Data Analysis
Version 1.52.0

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

AuthorColin A. Smith <csmith@scripps.edu>, Ralf Tautenhahn <rtautenh@gmail.com>, Steffen Neumann <sneumann@ipb-halle.de>, Paul Benton <hpbenton@scripps.edu>, Christopher Conley <cjconley@ucdavis.edu>, Johannes Rainer <Johannes.Rainer@eurac.edu>
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL (>= 2) + file LICENSE
Version1.52.0
URL http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("xcms")

Getting started

New and modified functionality in xcms

Popular man pages

diffreport-methods: Create report of analyte differences
findPeaks.centWave-methods: Feature detection for high resolution LC/MS data
getPeaks-methods: Get peak intensities for specified regions
group.density: Group peaks from different samples together
pval: Generate p-values for a vector of t-statistics
retcor.peakgroups-methods: Align retention times across samples
xcmsSet: Constructor for xcmsSet objects which finds peaks in...
See all...

All man pages Function index File listing

Man pages

absent-methods: Determine which peaks are absent / present in a sample class
adjustRtime: Alignment: Retention time correction methods.
adjustRtime-obiwarp: Align retention times across samples using Obiwarp
adjustRtime-peakGroups: Retention time correction based on alignment of house keeping...
AutoLockMass-methods: Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
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
calibrate: Calibrate peaks for correcting unprecise m/z values
Chromatogram-class: Representation of chromatographic MS data
chromatographic-peak-detection: Chromatographic peak detection methods.
collect-methods: Collect MS^n peaks into xcmsFragments
colMax: Find row and column maximum values
c.xcmsSet: Combine xcmsSet objects
descendZero: Find start and end points of a peak
diffreport-methods: Create report of analyte differences
do_adjustRtime_peakGroups: Align spectrum retention times across samples using peak...
do_findChromPeaks_centWave: Core API function for centWave peak detection
do_findChromPeaks_centWaveWithPredIsoROIs: Core API function for two-step centWave peak detection with...
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...
do_groupChromPeaks_density: Core API function for peak density based chromatographic peak...
do_groupChromPeaks_nearest: Core API function for chromatic peak grouping using a nearest...
do_groupPeaks_mzClust: Core API function for peak grouping using mzClust
doubleMatrix: Allocate double, integer, or logical matricies
etg: Empirically Transformed Gaussian function
extractChromatograms-method: Extracting chromatograms
fillChromPeaks: Integrate areas of missing peaks
fillPeaks.chrom-methods: Integrate areas of missing peaks
fillPeaks-methods: Integrate areas of missing peaks
fillPeaks.MSW-methods: Integrate areas of missing peaks in FTICR-MS data
filtfft: Apply an convolution filter using an FFT
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
findEqualGreater: Find values in sorted vectors
findMZ: Find fragment ions in xcmsFragment objects
findneutral: Find neutral losses in xcmsFragment objects
findPeaks.addPredictedIsotopeFeatures-methods: Feature detection based on predicted isotope features for...
findPeaks.centWave-methods: Feature detection for high resolution LC/MS data
findPeaks.centWaveWithPredictedIsotopeROIs-methods: Feature detection with centWave and additional isotope...
findPeaks.massifquant-methods: Feature detection for XC-MS data.
findPeaks.matchedFilter-xcmsRaw-method: Peak detection in the chromatographic time domain
findPeaks-methods: Feature detection for GC/MS and LC/MS Data - methods
findPeaks.MS1-methods: Collecting MS1 precursor peaks
findPeaks-MSW: Single-spectrum non-chromatography MS data peak detection
findPeaks.MSW-xcmsRaw-method: Peak detection for single-spectrum non-chromatography MS data
GenericParam: Generic parameter class
getEIC-methods: Get extracted ion chromatograms for specified m/z ranges
getPeaks-methods: Get peak intensities for specified regions
getScan-methods: Get m/z and intensity values for a single mass scan
getSpec-methods: Get average m/z and intensity values for multiple mass scans
getXcmsRaw-methods: Load the raw data for one or more files in the xcmsSet
groupChromPeaks: Correspondence: Chromatographic peak grouping methods.
groupChromPeaks-density: Peak grouping based on time dimension peak densities
groupChromPeaks-mzClust: High resolution peak grouping for single spectra samples
groupChromPeaks-nearest: Peak grouping based on proximity in the mz-rt space
group.density: Group peaks from different samples together
group-methods: Group peaks from different samples together
group.mzClust: Group Peaks via High Resolution Alignment
groupnames-methods: Generate unque names for peak groups
group.nearest: Group peaks from different samples together
groupval-methods: Extract a matrix of peak values for each group
image.xcmsRaw: Plot log intensity image of a xcmsRaw object
imputeLinInterpol: Impute values for empty elements in a vector using linear...
levelplot.xcmsRaw: Plot log intensity image of a xcmsRaw object
loadRaw-methods: Read binary data from a source
medianFilter: Apply a median filter to a matrix
msn2xcmsRaw: Copy MSn data in an xcmsRaw to the MS slots
na.flatfill: Fill in NA values at the extremes of a vector
panel.cor: Correlation coefficient panel for pairs function
peakPlots-methods: Plot a grid of a large number of peaks
peakTable-methods: Create report of aligned peak intensities
plotAdjustedRtime: Visualization of alignment results
plotChrom-methods: Plot extracted ion chromatograms from the profile matrix
plotEIC-methods: Plot extracted ion chromatograms for specified m/z range
plotPeaks-methods: Plot a grid of a large number of peaks
plotQC: Plot m/z and RT deviations for QC purposes without external...
plotRaw-methods: Scatterplot of raw data points
plotrt-methods: Plot retention time deviation profiles
plotScan-methods: Plot a single mass scan
plotSpec-methods: Plot mass spectra from the profile matrix
plotSurf-methods: Plot profile matrix 3D surface using OpenGL
plotTIC-methods: Plot total ion count
plot.xcmsEIC: Plot extracted ion chromatograms from multiple files
ProcessHistory-class: Tracking data processing
profGenerate: Generation of profile data
profMat-xcmsSet: The profile matrix
profMedFilt-methods: Median filtering of the profile matrix
profMethod-methods: Get and set method for generating profile data
profRange-methods: Specify a subset of profile mode data
profStep-methods: Get and set m/z step for generating profile data
pval: Generate p-values for a vector of t-statistics
rawEIC-methods: Get extracted ion chromatograms for specified m/z range
rawMat-methods: Get a raw data matrix
rectUnique: Determine a subset of rectangles with unique, non-overlapping...
retcor-methods: Correct retention time from different samples
retcor.obiwarp-methods: Align retention times across samples with Obiwarp
retcor.peakgroups-methods: Align retention times across samples
retexp: Set retention time window to a specified width
sampnames-methods: Get sample names
showError-xcmsSet-method: Extract processing errors
specDist.cosine-methods: a Distance function based on matching peaks
specDist.meanMZmatch-methods: a Distance function based on matching peaks
specDist-methods: Distance methods for xcmsSet, xcmsRaw and xsAnnotate
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.xcmsRaw: Divide an xcmsRaw object
split.xcmsSet: Divide an xcmsSet object
SSgauss: Gaussian Model
stitch-methods: Correct gaps in data
sub-xcmsRaw-logicalOrNumeric-missing-missing-method: Subset an xcmsRaw object by scans
updateObject-xcmsSet-method: Update an 'xcmsSet' object
useOriginalCode: Enable usage of old xcms code
verify.mzQuantML: Verify an mzQuantML file
write.cdf-methods: Save an xcmsRaw object to file
write.mzdata-methods: Save an xcmsRaw object to a file
write.mzQuantML: Save an xcmsSet object to an PSI mzQuantML file
writeMzTab: Save a grouped xcmsSet object in mzTab-1.1 format file
xcms-deprecated: Deprecated functions in package 'xcms'
xcmsEIC-class: Class xcmsEIC, a class for multi-sample extracted ion...
xcmsFileSource-class: Base class for loading raw data from a file
xcmsFragments: Constructor for xcmsFragments objects which holds Tandem MS...
xcmsFragments-class: Class xcmsFragments, a class for handling Tandem MS and...
XCMSnExp-class: Data container storing xcms preprocessing results
XCMSnExp-filter-methods: XCMSnExp filtering and subsetting
XCMSnExp-inherited-methods: XCMSnExp data manipulation methods inherited from MSnbase
XCMSnExp-peak-grouping-results: Accessing mz-rt feature data values
xcmsPapply: _Deprecated_: xcmsPapply
xcmsPeaks-class: A matrix of peaks
xcmsRaw: Constructor for xcmsRaw objects which reads NetCDF/mzXML...
xcmsRaw-class: Class xcmsRaw, a class for handling raw data
xcmsSet: Constructor for xcmsSet objects which finds peaks in...
xcmsSet-class: Class xcmsSet, a class for preprocessing peak data
xcmsSource-class: Virtual class for raw data sources
xcmsSource-methods: Create an 'xcmsSource' object in a flexible way

Functions

$,xcmsSet-method Man page
$<-,xcmsSet-method Man page
AutoLockMass Man page
AutoLockMass,xcmsRaw-method Man page
AutoLockMass-methods Man page
CentWaveParam Man page Source code
CentWaveParam-class Man page
CentWavePredIsoParam Man page Source code
CentWavePredIsoParam-class Man page
Chromatogram Man page Source code
Chromatogram-class Man page
FillChromPeaksParam Man page Source code
FillChromPeaksParam-class Man page
GenericParam Man page Man page Source code
GenericParam-class Man page
MSW Man page
MSW.cwt Source code
MSW.extendLength Source code
MSW.extendNBase Source code
MSW.getLocalMaximumCWT Source code
MSW.getRidge Source code
MSW.localMaximum Source code
MSWParam Man page Source code
MSWParam-class Man page
MSW_orig Source code Source code
MassifquantParam Man page Source code
MassifquantParam-class Man page
MatchedFilterParam Man page Source code
MatchedFilterParam-class Man page
MsFeatureData Man page
MsFeatureData-class Man page
MzClustParam Man page Source code
MzClustParam-class Man page
NearestPeaksParam Man page Source code
NearestPeaksParam-class Man page
ObiwarpParam Man page Source code
ObiwarpParam-class Man page
PeakDensityParam Man page Source code
PeakDensityParam-class Man page
PeakGroupsParam Man page Source code
PeakGroupsParam-class Man page
ProcessHistory Man page Source code
ProcessHistory-class Man page
SSgauss Man page
XCMSnExp Man page
XCMSnExp-class Man page Man page
XCMSnExp-filter Man page
XCMSnExp2xcmsSet Source code
XProcessHistory Man page Source code
XProcessHistory-class Man page
[,XCMSnExp,logicalOrNumeric,missing,missing-method Man page
[,xcmsRaw,logicalOrNumeric,missing,missing-method Man page
[,xcmsSet,ANY,ANY,ANY-method Man page
[,xcmsSet-method Man page
absMz Man page
absMz,MzClustParam-method Man page
absMz,NearestPeaksParam-method Man page
absMz<- Man page
absMz<-,MzClustParam-method Man page
absMz<-,NearestPeaksParam-method Man page
absRt Man page
absRt,NearestPeaksParam-method Man page
absRt<- Man page
absRt<-,NearestPeaksParam-method Man page
absent Man page
absent,xcmsSet-method Man page
addParams Man page
addParams,MSWParam-method Man page
addParams<- Man page
addParams<-,MSWParam-method Man page
adjustRtime Man page
adjustRtime,OnDiskMSnExp,ObiwarpParam-method Man page
adjustRtime,XCMSnExp,ObiwarpParam-method Man page
adjustRtime,XCMSnExp,PeakGroupsParam-method Man page
adjustRtime-obiwarp Man page
adjustRtime-peakGroups Man page
adjustRtimePeakGroups Man page Source code
adjustedRtime Man page
adjustedRtime,MsFeatureData-method Man page
adjustedRtime,XCMSnExp-method Man page
adjustedRtime<- Man page
adjustedRtime<-,MsFeatureData-method Man page
adjustedRtime<-,XCMSnExp-method Man page
aggregateMethod2int Source code
aggregationFun Man page
aggregationFun,Chromatogram-method Man page
ampTh Man page
ampTh,MSWParam-method Man page
ampTh<- Man page
ampTh<-,MSWParam-method Man page
applyRtAdjToChromPeaks Source code
applyRtAdjustment Source code
as.data.frame,Chromatogram-method Man page
baseValue Man page
baseValue,MatchedFilterParam-method Man page
baseValue<- Man page
baseValue<-,MatchedFilterParam-method Man page
bin,XCMSnExp-method Man page
binSize Man page
binSize,MatchedFilterParam-method Man page
binSize,ObiwarpParam-method Man page
binSize,PeakDensityParam-method Man page
binSize<- Man page
binSize<-,MatchedFilterParam-method Man page
binSize<-,ObiwarpParam-method Man page
binSize<-,PeakDensityParam-method Man page
binYonX Man page Source code
breaks_on_binSize Man page Source code
breaks_on_nBins Man page Source code
buildAnalysisSummary Source code
buildAssayList Source code
buildAuditCollection Source code
buildCVlist Source code
buildCvParams Source code
buildDataProcessingList Source code
buildFeatureList Source code
buildInputFiles Source code
buildMzq Source code
buildSmallMoleculeList Source code
buildSoftwareList Source code
buildStudyVariableList Source code
bw Man page
bw,PeakDensityParam-method Man page
bw<- Man page
bw<-,PeakDensityParam-method Man page
c, c-methods Man page
c.xcmsSet Man page Source code
calibrate Man page
calibrate,xcmsSet-method Man page
cent Source code
centWave Man page
centWaveWithPredIsoROIs Man page
centWave_new Source code
centWave_orig Source code
centerSample Man page
centerSample,ObiwarpParam-method Man page
centerSample<- Man page
centerSample<-,ObiwarpParam-method Man page
checkBack Man page
checkBack,MassifquantParam-method Man page
checkBack<- Man page
checkBack<-,MassifquantParam-method Man page
chromPeaks Man page
chromPeaks,MsFeatureData-method Man page
chromPeaks,XCMSnExp-method Man page
chromPeaks<- Man page
chromPeaks<-,MsFeatureData-method Man page
chromPeaks<-,XCMSnExp-method Man page
chromatographic-peak-detection Man page
clean,XCMSnExp-method Man page
colMax Man page Source code
collect Man page
collect,xcmsFragments-method Man page
collect,xcmsRaw-method Man page
collect-methods Man page
consecMissedLimit Man page
consecMissedLimit,MassifquantParam-method Man page
consecMissedLimit<- Man page
consecMissedLimit<-,MassifquantParam-method Man page
continuousPtsAboveThreshold Source code
continuousPtsAboveThresholdIdx Source code
copy_env Source code
createProfileMatrix Source code
criticalValue Man page
criticalValue,MassifquantParam-method Man page
criticalValue<- Man page
criticalValue<-,MassifquantParam-method Man page
cvTerm Source code
deepCopy Man page
deepCopy,xcmsRaw-method Man page
defineColAndTy Source code
descendMin Man page Source code
descendMinTol Source code
descendValue Man page Source code
descendZero Man page Source code
diffreport Man page
diffreport,xcmsSet-method Man page
distFun Man page
distFun,ObiwarpParam-method Man page
distFun<- Man page
distFun<-,ObiwarpParam-method Man page
distance Man page
distance,MatchedFilterParam-method Man page
distance<- Man page
distance<-,MatchedFilterParam-method Man page
do_adjustRtime_peakGroups Man page Source code
do_adjustRtime_peakGroups_orig Source code
do_define_adducts Source code
do_define_isotopes Source code
do_findChromPeaks_addPredIsoROIs Man page Source code
do_findChromPeaks_addPredIsoROIs_mod Source code
do_findChromPeaks_centWave Man page Source code
do_findChromPeaks_centWaveWithPredIsoROIs Man page Source code
do_findChromPeaks_massifquant Man page Source code
do_findChromPeaks_matchedFilter Man page Source code
do_findKalmanROI Source code
do_findPeaks_MSW Man page Source code
do_groupChromPeaks_density Man page Source code
do_groupChromPeaks_density_par Source code
do_groupChromPeaks_nearest Man page Source code
do_groupPeaks_mzClust Man page Source code
doubleMatrix Man page Source code
dropAdjustedRtime Man page
dropAdjustedRtime,MsFeatureData-method Man page
dropAdjustedRtime,XCMSnExp-method Man page
dropChromPeaks Man page
dropChromPeaks,MsFeatureData-method Man page
dropChromPeaks,XCMSnExp-method Man page
dropFeatureDefinitions Man page
dropFeatureDefinitions,MsFeatureData-method Man page
dropFeatureDefinitions,XCMSnExp-method Man page
dropFilledChromPeaks Man page
dropFilledChromPeaks,XCMSnExp-method Man page
dropProcessHistories Source code
dropProcessHistoriesList Source code
estimate Source code
estimateChromNoise Source code
etg Man page Source code
expandMz Man page
expandMz,FillChromPeaksParam-method Man page
expandMz<- Man page
expandMz<-,FillChromPeaksParam-method Man page
expandRt Man page
expandRt,FillChromPeaksParam-method Man page
expandRt<- Man page
expandRt<-,FillChromPeaksParam-method Man page
extraPeaks Man page
extraPeaks,PeakGroupsParam-method Man page
extraPeaks<- Man page
extraPeaks<-,PeakGroupsParam-method Man page
extractChromatogram Source code
extractChromatograms Man page
extractChromatograms,OnDiskMSnExp-method Man page
extractChromatograms,XCMSnExp-method Man page
extractMsData Source code
factorDiag Man page
factorDiag,ObiwarpParam-method Man page
factorDiag<- Man page
factorDiag<-,ObiwarpParam-method Man page
factorGap Man page
factorGap,ObiwarpParam-method Man page
factorGap<- Man page
factorGap<-,ObiwarpParam-method Man page
family Man page
family,PeakGroupsParam-method Man page
family<- Man page
family<-,PeakGroupsParam-method Man page
fastMatch Source code
featureDefinitions Man page
featureDefinitions,MsFeatureData-method Man page
featureDefinitions,XCMSnExp-method Man page
featureDefinitions<- Man page
featureDefinitions<-,MsFeatureData-method Man page
featureDefinitions<-,XCMSnExp-method Man page
featureIDs Source code
featureValues Man page
featureValues,XCMSnExp-method Man page
fileIndex Man page
fileIndex,ProcessHistory-method Man page
filepaths Man page
filepaths,xcmsSet-method Man page
filepaths<- Man page
filepaths<-,xcmsSet-method Man page
fillChromPeaks Man page
fillChromPeaks,XCMSnExp,FillChromPeaksParam-method Man page
fillChromPeaks,XCMSnExp,missing-method Man page
fillPeaks Man page
fillPeaks,xcmsSet-method Man page
fillPeaks-methods Man page
fillPeaks.MSW Man page
fillPeaks.MSW,xcmsSet-method Man page
fillPeaks.MSW-methods Man page
fillPeaks.chrom Man page
fillPeaks.chrom,xcmsSet-method Man page
fillPeaks.chrom-methods Man page
fillPeaksChromPar Source code
filterAcquisitionNum,XCMSnExp-method Man page
filterChromPeaks Source code
filterFile,XCMSnExp-method Man page
filterMsLevel,XCMSnExp-method Man page
filterMz,XCMSnExp-method Man page
filterRt,Chromatogram-method Man page
filterRt,XCMSnExp-method Man page
filtfft Man page Source code
findChromPeaks Man page
findChromPeaks,OnDiskMSnExp,CentWaveParam-method Man page
findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam-method Man page
findChromPeaks,OnDiskMSnExp,MSWParam-method Man page
findChromPeaks,OnDiskMSnExp,MassifquantParam-method Man page
findChromPeaks,OnDiskMSnExp,MatchedFilterParam-method Man page
findChromPeaks,XCMSnExp,ANY-method Man page
findChromPeaks-centWave Man page
findChromPeaks-centWaveWithPredIsoROIs Man page
findChromPeaks-massifquant Man page
findChromPeaks-matchedFilter Man page
findChromPeaksInFile Source code
findChromPeaks_OnDiskMSnExp Source code
findChromPeaks_Spectrum_list Source code
findEqualGreater Man page Source code
findEqualGreaterM Man page Source code
findEqualGreaterUnsorted Source code
findEqualLess Man page Source code
findMZ Man page
findMZ,xcmsFragments-method Man page
findPeaks Man page
findPeaks,xcmsRaw-method Man page
findPeaks-MSW Man page
findPeaks-methods Man page
findPeaks.MS1 Man page
findPeaks.MS1,xcmsRaw-method Man page
findPeaks.MSW Man page
findPeaks.MSW,xcmsRaw-method Man page
findPeaks.addPredictedIsotopeFeatures Man page
findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method Man page
findPeaks.centWave Man page
findPeaks.centWave,xcmsRaw-method Man page
findPeaks.centWaveWithPredictedIsotopeROIs Man page
findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method Man page
findPeaks.massifquant Man page
findPeaks.massifquant,xcmsRaw-method Man page
findPeaks.matchedFilter Man page
findPeaks.matchedFilter,xcmsRaw-method Man page
findPeaksPar Source code
findPeaks_MSW_OnDiskMSnExp Source code
findPeaks_MSW_Spectrum_list Source code
findRange Man page Source code
findneutral Man page
findneutral,xcmsFragments-method Man page
firstBaselineCheck Man page
firstBaselineCheck,CentWaveParam-method Man page
firstBaselineCheck<- Man page
firstBaselineCheck<-,CentWaveParam-method Man page
fitGauss Source code
fitModel Source code
fitgauss Man page
fitgauss,CentWaveParam-method Man page
fitgauss,MassifquantParam-method Man page
fitgauss<- Man page
fitgauss<-,CentWaveParam-method Man page
fitgauss<-,MassifquantParam-method Man page
fromFile,Chromatogram-method Man page
fwhm Man page
fwhm,MatchedFilterParam-method Man page
fwhm<- Man page
fwhm<-,MatchedFilterParam-method Man page
gapExtend Man page
gapExtend,ObiwarpParam-method Man page
gapExtend<- Man page
gapExtend<-,ObiwarpParam-method Man page
gapInit Man page
gapInit,ObiwarpParam-method Man page
gapInit<- Man page
gapInit<-,ObiwarpParam-method Man page
gauss Source code
gaussCoverage Source code
getChromPeakData Source code
getChromPeakData_matchedFilter Source code
getEIC Man page
getEIC,xcmsRaw-method Man page
getEIC,xcmsSet-method Man page
getEIC-methods Man page Man page
getEICNew Source code
getEICOld Source code
getLocalNoiseEstimate Source code
getMSWPeakData Source code
getMSWPeakData2 Source code
getMsnScan Man page
getMsnScan,xcmsRaw-method Man page
getPeakGroupsRtMatrix Source code
getPeakInt Source code
getPeakInt2 Source code
getPeakInt3 Source code
getPeaks Man page
getPeaks,xcmsRaw-method Man page
getPeaks-methods Man page
getPeaks_new Source code
getPeaks_orig Source code
getProcessErrors Source code
getProcessHistory Source code
getScan Man page
getScan,xcmsRaw-method Man page
getSpec Man page
getSpec,xcmsRaw-method Man page
getSpec-methods Man page
getSpecWindow Source code
getXS Source code
getXcmsRaw Man page
getXcmsRaw,xcmsSet-method Man page
getdeviations Source code
group Man page
group,xcmsSet-method Man page
group-methods Man page
group.density Man page
group.density,xcmsSet-method Man page
group.mzClust Man page
group.mzClust,xcmsSet-method Man page
group.nearest Man page
group.nearest,xcmsSet-method Man page
groupChromPeaks Man page
groupChromPeaks,XCMSnExp,MzClustParam-method Man page
groupChromPeaks,XCMSnExp,NearestPeaksParam-method Man page
groupChromPeaks,XCMSnExp,PeakDensityParam-method Man page
groupChromPeaks-density Man page
groupChromPeaks-mzClust Man page
groupChromPeaks-nearest Man page
groupidx Man page
groupidx,xcmsSet-method Man page
groupidx<- Man page
groupidx<-,xcmsSet-method Man page
groupnames Man page
groupnames,xcmsEIC-method Man page
groupnames,xcmsSet-method Man page
groupnames-methods Man page
groups Man page
groups,xcmsSet-method Man page
groups<- Man page
groups<-,xcmsSet-method Man page
groupval Man page
groupval,xcmsSet-method Man page
groupval-methods Man page
hasAdjustedRtime Man page
hasAdjustedRtime,MsFeatureData-method Man page
hasAdjustedRtime,XCMSnExp-method Man page
hasChromPeaks Man page
hasChromPeaks,MsFeatureData-method Man page
hasChromPeaks,XCMSnExp-method Man page
hasFeatures Man page
hasFeatures,MsFeatureData-method Man page
hasFeatures,XCMSnExp-method Man page
hasFilledPeaks Source code
image,xcmsRaw-method Man page
impute,MatchedFilterParam-method Man page
impute<- Man page
impute<-,MatchedFilterParam-method Man page
imputeLinInterpol Man page Source code
index Man page
index,MatchedFilterParam-method Man page
index<- Man page
index<-,MatchedFilterParam-method Man page
initPenalty Man page
initPenalty,ObiwarpParam-method Man page
initPenalty<- Man page
initPenalty<-,ObiwarpParam-method Man page
integerMatrix Man page Source code
integrate,CentWaveParam-method Man page
integrate,MassifquantParam-method Man page
integrate<- Man page
integrate<-,CentWaveParam-method Man page
integrate<-,MassifquantParam-method Man page
intensity,Chromatogram-method Man page
intensity,XCMSnExp-method Man page
invalid Source code
isCdfFile Source code
isMzMLFile Source code
isRampFile Source code
joinOverlappingPeaks Source code
kNN Man page
kNN,NearestPeaksParam-method Man page
kNN<- Man page
kNN<-,NearestPeaksParam-method Man page
length,Chromatogram-method Man page
levelplot Man page
levelplot,xcmsRaw-method Man page
levelplot,xcmsSet-method Man page
loadRaw Man page
loadRaw,xcmsFileSource-method Man page
loadRaw,xcmsSource-method Man page
loadRaw-methods Man page
localAlignment Man page
localAlignment,ObiwarpParam-method Man page
localAlignment<- Man page
localAlignment<-,ObiwarpParam-method Man page
logicalMatrix Man page Source code
makeacqNum Man page
makeacqNum, xcmsRaw-method Man page
massifquant Man page
match.profFun Source code
matchedFilter Man page
matchedFilter_binYonX_no_iter Source code
matchedFilter_orig Source code
matchpeaks Source code
max,MatchedFilterParam-method Man page
max<- Man page
max<-,MatchedFilterParam-method Man page
maxCharge Man page
maxCharge,CentWavePredIsoParam-method Man page
maxCharge<- Man page
maxCharge<-,CentWavePredIsoParam-method Man page
maxFeatures Man page
maxFeatures,PeakDensityParam-method Man page
maxFeatures<- Man page
maxFeatures<-,PeakDensityParam-method Man page
maxIso Man page
maxIso,CentWavePredIsoParam-method Man page
maxIso<- Man page
maxIso<-,CentWavePredIsoParam-method Man page
medianFilter Man page Source code
minFraction Man page
minFraction,MzClustParam-method Man page
minFraction,PeakDensityParam-method Man page
minFraction,PeakGroupsParam-method Man page
minFraction<- Man page
minFraction<-,MzClustParam-method Man page
minFraction<-,PeakDensityParam-method Man page
minFraction<-,PeakGroupsParam-method Man page
minNoiseLevel Man page
minNoiseLevel,MSWParam-method Man page
minNoiseLevel<- Man page
minNoiseLevel<-,MSWParam-method Man page
minSamples Man page
minSamples,MzClustParam-method Man page
minSamples,PeakDensityParam-method Man page
minSamples<- Man page
minSamples<-,MzClustParam-method Man page
minSamples<-,PeakDensityParam-method Man page
minifm Source code
mpute2method Source code
mputeMethod2int Source code
msgfun.featureDetection Source code
msgfunGeneric Source code
mslevel Man page
mslevel,xcmsRaw-method Man page
mslevel,xcmsSet-method Man page
msn2xcmsRaw Man page Source code
mz,Chromatogram-method Man page
mz,XCMSnExp-method Man page
mzCenter.apex Source code
mzCenter.mean Source code
mzCenter.meanApex3 Source code
mzCenter.wMean Source code
mzCenter.wMeanApex3 Source code
mzCenterFun Man page
mzCenterFun,CentWaveParam-method Man page
mzCenterFun,MassifquantParam-method Man page
mzCenterFun<- Man page
mzCenterFun<-,CentWaveParam-method Man page
mzCenterFun<-,MassifquantParam-method Man page
mzClustGeneric Source code
mzClust_hclust Source code
mzFileType Source code
mzIntervalExtension Man page
mzIntervalExtension,CentWavePredIsoParam-method Man page
mzIntervalExtension<- Man page
mzIntervalExtension<-,CentWavePredIsoParam-method Man page
mzTabAddComment Source code
mzTabAddSME Source code
mzTabAddTagValue Source code
mzTabAddValues Source code
mzTabHeader Source code
mzVsRtBalance Man page
mzVsRtBalance,NearestPeaksParam-method Man page
mzVsRtBalance<- Man page
mzVsRtBalance<-,NearestPeaksParam-method Man page
mzdiff Man page
mzdiff,CentWaveParam-method Man page
mzdiff,MassifquantParam-method Man page
mzdiff,MatchedFilterParam-method Man page
mzdiff<- Man page
mzdiff<-,CentWaveParam-method Man page
mzdiff<-,MassifquantParam-method Man page
mzdiff<-,MatchedFilterParam-method Man page
mzrange Man page
mzrange,xcmsEIC-method Man page
na.flatfill Man page Source code
nearbyPeak Man page
nearbyPeak,MSWParam-method Man page
nearbyPeak<- Man page
nearbyPeak<-,MSWParam-method Man page
netCDFClose Source code
netCDFIsFile Source code
netCDFMSPoints Source code
netCDFOpen Source code
netCDFRawData Source code
netCDFStrError Source code
netCDFVarDouble Source code
netCDFVarID Source code
netCDFVarInt Source code
netCDFVarLen Source code
noise Man page
noise,CentWaveParam-method Man page
noise,MassifquantParam-method Man page
noise<- Man page
noise<-,CentWaveParam-method Man page
noise<-,MassifquantParam-method Man page
normalize,XCMSnExp-method Man page
obiwarp Source code
odd Source code
onAttach Source code
onLoad Source code
onUnload Source code
pSet2xcmsSet Source code
panel.cor Man page Source code
param2list Source code
param2string Source code
patternVsRowScore Source code
peakGroupsMatrix Man page
peakGroupsMatrix,PeakGroupsParam-method Man page
peakGroupsMatrix<- Man page
peakGroupsMatrix<-,PeakGroupsParam-method Man page
peakIndex Source code
peakPlots,xcmsSet-method Man page
peakPlots-methods Man page
peakScaleRange Man page
peakScaleRange,MSWParam-method Man page
peakScaleRange<- Man page
peakScaleRange<-,MSWParam-method Man page
peakTable Man page
peakTable,xcmsSet-method Man page
peakThr Man page
peakThr,MSWParam-method Man page
peakThr<- Man page
peakThr<-,MSWParam-method Man page
peaks Man page
peaks,xcmsSet-method Man page
peaks<- Man page
peaks<-,xcmsSet-method Man page
peakwidth Man page
peakwidth,CentWaveParam-method Man page
peakwidth,MassifquantParam-method Man page
peakwidth<- Man page
peakwidth<-,CentWaveParam-method Man page
peakwidth<-,MassifquantParam-method Man page
phenoData Man page
phenoData,xcmsSet-method Man page
phenoData<- Man page
phenoData<-,xcmsSet,ANY-method Man page
phenoData<-,xcmsSet-method Man page
phenoDataFromPaths Source code
pickPeaks,XCMSnExp-method Man page
plot, plot-methods Man page
plot.xcmsEIC Man page Source code
plotAdjustedRtime Man page Source code
plotChrom Man page
plotChrom,xcmsRaw-method Man page
plotChrom-methods Man page
plotEIC Man page
plotEIC,xcmsRaw-method Man page
plotPeaks Man page
plotPeaks,xcmsRaw-method Man page
plotPeaks-methods Man page
plotQC Man page Source code
plotRaw Man page
plotRaw,xcmsRaw-method Man page
plotRaw-methods Man page
plotScan Man page
plotScan,xcmsRaw-method Man page
plotScan-methods Man page
plotSpec Man page
plotSpec,xcmsRaw-method Man page
plotSpec-methods Man page
plotSpecWindow Source code
plotSurf Man page
plotSurf,xcmsRaw-method Man page
plotSurf-methods Man page
plotTIC Man page
plotTIC,xcmsRaw-method Man page
plotTIC-methods Man page
plotTree Man page
plotTree,xcmsFragments-method Man page
plotrt Man page
plotrt,xcmsSet-method Man page
plotrt-methods Man page
polarity,CentWavePredIsoParam-method Man page
polarity<- Man page
polarity<-,CentWavePredIsoParam-method Man page
ppm Man page Source code
ppm,CentWaveParam-method Man page
ppm,FillChromPeaksParam-method Man page
ppm,MassifquantParam-method Man page
ppm,MzClustParam-method Man page
ppm<- Man page
ppm<-,CentWaveParam-method Man page
ppm<-,FillChromPeaksParam-method Man page
ppm<-,MassifquantParam-method Man page
ppm<-,MzClustParam-method Man page
ppmDev Source code
precursorMz,Chromatogram-method Man page
prefilter Man page
prefilter,CentWaveParam-method Man page
prefilter,MassifquantParam-method Man page
prefilter<- Man page
prefilter<-,CentWaveParam-method Man page
prefilter<-,MassifquantParam-method Man page
present Man page
present,xcmsSet-method Man page
processDate Man page
processDate,ProcessHistory-method Man page
processHistory Man page
processHistory,XCMSnExp-method Man page
processHistoryTypes Man page Source code
processInfo Man page
processInfo,ProcessHistory-method Man page
processParam Man page
processParam,XProcessHistory-method Man page
processResultList Source code
processType Man page
processType,ProcessHistory-method Man page
productMz Man page
productMz,Chromatogram-method Man page
profBin Man page Source code
profBinLin Man page Source code
profBinLinBase Man page Source code
profBinLinBaseM Man page Source code
profBinLinM Man page Source code
profBinM Man page Source code
profBinR Source code
profEIC Source code
profEIC2 Source code
profIntLin Man page Source code
profIntLinM Man page Source code
profMat Man page
profMat,OnDiskMSnExp-method Man page
profMat,XCMSnExp-method Man page
profMat,xcmsRaw-method Man page
profMat-xcmsSet Man page
profMaxIdx Man page Source code
profMaxIdxM Man page Source code
profMedFilt Man page
profMedFilt,xcmsRaw-method Man page
profMedFilt-methods Man page
profMethod Man page
profMethod,xcmsRaw-method Man page
profMethod,xcmsSet-method Man page
profMethod-methods Man page
profMethod<- Man page
profMethod<-,xcmsRaw-method Man page
profMethod<--methods Man page
profMz Man page
profMz,xcmsRaw-method Man page
profRange Man page
profRange,xcmsRaw-method Man page
profRange-methods Man page
profStep Man page
profStep,xcmsRaw-method Man page
profStep,xcmsSet-method Man page
profStep-methods Man page
profStep<- Man page
profStep<-,xcmsRaw-method Man page
profStep<--methods Man page
profile-matrix Man page
profinfo Man page
profinfo,xcmsRaw-method Man page
profinfo,xcmsSet-method Man page
profinfo<- Man page
profinfo<-,xcmsSet-method Man page
progressCallback Man page
progressCallback,xcmsSet-method Man page
progressCallback<- Man page
progressCallback<-,xcmsSet-method Man page
pval Man page Source code
rawEIC Man page
rawEIC,xcmsRaw-method Man page
rawMat Man page Source code
rawMat,xcmsRaw-method Man page
rawMat-methods Man page
rawMat2 Source code
rbind.ragged Source code
read.mascot Source code
readRawData Source code
rectUnique Man page Source code
remakeTIC Source code
removePeaks,XCMSnExp-method Man page
response Man page
response,ObiwarpParam-method Man page
response<- Man page
response<-,ObiwarpParam-method Man page
retcor Man page
retcor,xcmsSet-method Man page
retcor-methods Man page
retcor.linear Man page
retcor.linear,xcmsSet-method Man page
retcor.loess Man page
retcor.loess,xcmsSet-method Man page
retcor.obiwarp Man page
retcor.obiwarp,xcmsSet-method Man page
retcor.peakgroups Man page
retcor.peakgroups,xcmsSet-method Man page
retcor.peakgroups_orig Source code
retexp Man page Source code
revMz Man page
revMz,xcmsRaw-method Man page
ridgeLength Man page
ridgeLength,MSWParam-method Man page
ridgeLength<- Man page
ridgeLength<-,MSWParam-method Man page
roiList Man page
roiList,CentWaveParam-method Man page
roiList<- Man page
roiList<-,CentWaveParam-method Man page
roiScales Man page
roiScales,CentWaveParam-method Man page
roiScales<- Man page
roiScales<-,CentWaveParam-method Man page
rowMax Man page Source code
rtime,Chromatogram-method Man page
rtime,XCMSnExp-method Man page
rtrange Man page
rtrange,xcmsEIC-method Man page
running Source code
sampclass Man page
sampclass,xcmsSet-method Man page
sampclass<- Man page
sampclass<-,xcmsSet-method Man page
sampleGroups Man page
sampleGroups,MzClustParam-method Man page
sampleGroups,NearestPeaksParam-method Man page
sampleGroups,PeakDensityParam-method Man page
sampleGroups<- Man page
sampleGroups<-,MzClustParam-method Man page
sampleGroups<-,NearestPeaksParam-method Man page
sampleGroups<-,PeakDensityParam-method Man page
sampnames Man page
sampnames,xcmsEIC-method Man page
sampnames,xcmsSet-method Man page
sampnames-methods Man page
sampnames<- Man page
sampnames<-,xcmsSet-method Man page
scales Man page
scales,MSWParam-method Man page
scales<- Man page
scales<-,MSWParam-method Man page
scanrange Man page
scanrange,xcmsRaw-method Man page
scanrange,xcmsSet-method Man page
sequences Source code
setAs Man page
setXCMSOptions Source code
show,CentWaveParam-method Man page
show,CentWavePredIsoParam-method Man page
show,Chromatogram-method Man page
show,FillChromPeaksParam-method Man page
show,GenericParam-method Man page
show,MSWParam-method Man page
show,MassifquantParam-method Man page
show,MatchedFilterParam-method Man page
show,MsFeatureData-method Man page
show,MzClustParam-method Man page
show,NearestPeaksParam-method Man page
show,ObiwarpParam-method Man page
show,PeakDensityParam-method Man page
show,PeakGroupsParam-method Man page
show,ProcessHistory-method Man page
show,XCMSnExp-method Man page
show,XProcessHistory-method Man page
show,xcmsEIC-method Man page
show,xcmsFragments-method Man page
show,xcmsPeaks-method Man page
show,xcmsRaw-method Man page
show,xcmsSet-method Man page
showError Man page
showError,xcmsSet-method Man page
sigma Man page
sigma,MatchedFilterParam-method Man page
sigma<- Man page
sigma<-,MatchedFilterParam-method Man page
sliceApply Source code
smooth Man page
smooth,PeakGroupsParam-method Man page
smooth,XCMSnExp-method Man page
smooth<- Man page
smooth<-,PeakGroupsParam-method Man page
snthresh Man page
snthresh,CentWaveParam-method Man page
snthresh,MSWParam-method Man page
snthresh,MassifquantParam-method Man page
snthresh,MatchedFilterParam-method Man page
snthresh<- Man page
snthresh<-,CentWaveParam-method Man page
snthresh<-,MSWParam-method Man page
snthresh<-,MassifquantParam-method Man page
snthresh<-,MatchedFilterParam-method Man page
snthreshIsoROIs Man page
snthreshIsoROIs,CentWavePredIsoParam-method Man page
snthreshIsoROIs<- Man page
snthreshIsoROIs<-,CentWavePredIsoParam-method Man page
sortMz Man page
sortMz,xcmsRaw-method Man page
span Man page
span,PeakGroupsParam-method Man page
span<- Man page
span<-,PeakGroupsParam-method Man page
specDist Man page
specDist,xcmsSet-method Man page
specDist-methods Man page
specDist.cosine Man page
specDist.cosine,matrix,matrix-method Man page
specDist.meanMZmatch Man page
specDist.meanMZmatch,matrix,matrix-method Man page
specDist.peakCount Man page
specDist.peakCount,matrix,matrix-method Man page
specDist.peakCount-methods Man page
specNoise Man page Source code
specPeaks Man page Source code
spectra,XCMSnExp-method Man page
spectraSubsets Source code
split, split-methods Man page
split.xcmsRaw Man page Source code
split.xcmsSet Man page Source code
steps Man page
steps,MatchedFilterParam-method Man page
steps<- Man page
steps<-,MatchedFilterParam-method Man page
stitch Man page
stitch,xcmsRaw-method Man page
stitch-methods Man page
stitch.netCDF Man page
stitch.xml Man page
subset-xcmsRaw Man page
testIntegerInput Source code
testRealInput Source code
trimm Source code
tuneIn Man page
tuneIn,MSWParam-method Man page
tuneIn<- Man page
tuneIn<-,MSWParam-method Man page
unions Man page
unions,MassifquantParam-method Man page
unions<- Man page
unions<-,MassifquantParam-method Man page
updateFileIndex Source code
updateObject,xcmsSet-method Man page
useOriginalCode Man page Source code
validChromPeaksMatrix Source code
validChromatogram Source code
validProcessHistory Source code
validateMsFeatureData Source code
valueCount2ScanIndex Source code
verboseColumns Man page
verboseColumns,CentWaveParam-method Man page
verboseColumns,MSWParam-method Man page
verboseColumns,MassifquantParam-method Man page
verboseColumns<- Man page
verboseColumns<-,CentWaveParam-method Man page
verboseColumns<-,MSWParam-method Man page
verboseColumns<-,MassifquantParam-method Man page
verify.mzQuantML Man page Source code
which.colMax Man page Source code
which.rowMax Man page Source code
withWave Man page
withWave,MassifquantParam-method Man page
withWave<- Man page
withWave<-,MassifquantParam-method Man page
write.cdf Man page
write.cdf,xcmsRaw-method Man page
write.metaboanalyst Source code
write.mzQuantML Man page
write.mzQuantML,xcmsSet-method Man page
write.mzdata Man page
write.mzdata,xcmsRaw-method Man page
writeMzTab Man page Source code
xcms-deprecated Man page
xcmsBoxPlot Source code
xcmsClusterApply Source code
xcmsEIC-class Man page
xcmsFileSource-class Man page
xcmsFragments Man page Source code
xcmsFragments-class Man page
xcmsFragments.collect Source code
xcmsFragments.hasMSn Source code
xcmsFragments.makeXS Source code
xcmsFragments.plotTree Source code
xcmsFragments.show Source code
xcmsPapply Man page
xcmsParallelSetup Source code
xcmsPeaks-class Man page
xcmsRaw Man page Source code
xcmsRaw-class Man page
xcmsSet Man page Source code
xcmsSet-class Man page
xcmsSource Man page
xcmsSource,character-method Man page
xcmsSource,xcmsSource-method Man page
xcmsSource-class Man page
xcmsSource-methods Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/AllGenerics.R
R/DataClasses.R
R/Deprecated.R
R/MPI.R
R/c.R
R/cwTools.R
R/databases.R
R/do_adjustRtime-functions.R
R/do_findChromPeaks-functions.R
R/do_groupChromPeaks-functions.R
R/fastMatch.R
R/functions-Chromatogram.R
R/functions-IO.R
R/functions-MsFeatureData.R
R/functions-OnDiskMSnExp.R
R/functions-Params.R
R/functions-ProcessHistory.R
R/functions-XCMSnExp.R
R/functions-binning.R
R/functions-normalization.R
R/functions-utils.R
R/functions-xcmsEIC.R
R/functions-xcmsFragments.R
R/functions-xcmsRaw.R
R/functions-xcmsSet.R
R/init.R
R/matchpeaks.R
R/methods-Chromatogram.R
R/methods-IO.R
R/methods-MsFeatureData.R
R/methods-OnDiskMSnExp.R
R/methods-Params.R
R/methods-ProcessHistory.R
R/methods-XCMSnExp.R
R/methods-netCdfSource.R
R/methods-rampSource.R
R/methods-xcmsEIC.R
R/methods-xcmsFileSource.R
R/methods-xcmsFragments.R
R/methods-xcmsPeaks.R
R/methods-xcmsRaw.R
R/methods-xcmsSet.R
R/models.R
R/msn2xcmsRaw.R
R/mzClust.R
R/netCDF.R
R/plotQC.R
R/ramp.R
R/specDist.R
R/unix
R/windows
R/write.mzquantML.R
R/writemzdata.R
R/writemztab.R
R/xcmsSource.R
R/zzz.R
build
build/vignette.rds
inst
inst/CHANGELOG
inst/CITATION
inst/NEWS
inst/doc
inst/doc/new_functionality.R
inst/doc/new_functionality.Rmd
inst/doc/new_functionality.html
inst/doc/xcmsDirect.R
inst/doc/xcmsDirect.Rnw
inst/doc/xcmsDirect.pdf
inst/doc/xcmsInstall.Rnw
inst/doc/xcmsInstall.pdf
inst/doc/xcmsMSn.R
inst/doc/xcmsMSn.Rnw
inst/doc/xcmsMSn.pdf
inst/doc/xcmsPreprocess.R
inst/doc/xcmsPreprocess.Rnw
inst/doc/xcmsPreprocess.pdf
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/mzQuantML_1_0_0.xsd
inst/unitTests/runit.BiocParallel.R
inst/unitTests/runit.Chromatogram.R
inst/unitTests/runit.Param-classes.R
inst/unitTests/runit.XCMSnExp.R
inst/unitTests/runit.absentPresent.R
inst/unitTests/runit.binning.R
inst/unitTests/runit.createProfileMatrix.R
inst/unitTests/runit.diffreport.R
inst/unitTests/runit.do_adjustRtime.R
inst/unitTests/runit.do_findChromPeaks_MSW.R
inst/unitTests/runit.do_findChromPeaks_centWave.R
inst/unitTests/runit.do_findChromPeaks_centWave_isotopes.R
inst/unitTests/runit.do_findChromPeaks_massifquant.R
inst/unitTests/runit.do_findChromPeaks_matchedFilter.R
inst/unitTests/runit.do_groupChromPeaks.R
inst/unitTests/runit.fillChromPeaks.R
inst/unitTests/runit.fillPeaks.R
inst/unitTests/runit.findPeaksCentWave.R
inst/unitTests/runit.findPeaksCentWave.fitGauss.plot.R
inst/unitTests/runit.findPeaksCentWaveWithIsotopeROIs.R
inst/unitTests/runit.findPeaksMassIfQuant.R
inst/unitTests/runit.getEIC.R
inst/unitTests/runit.getXcmsRaw.R
inst/unitTests/runit.group.R
inst/unitTests/runit.msms.R
inst/unitTests/runit.new_read_data.R
inst/unitTests/runit.new_scanrange_subsetting.R
inst/unitTests/runit.obiwarp.R
inst/unitTests/runit.phenoData.R
inst/unitTests/runit.processHistory.R
inst/unitTests/runit.profStepPad.R
inst/unitTests/runit.ramp.R
inst/unitTests/runit.rawMat.R
inst/unitTests/runit.sampclass.R
inst/unitTests/runit.scanrage.R
inst/unitTests/runit.snames.R
inst/unitTests/runit.specDist.R
inst/unitTests/runit.splitCombine.R
inst/unitTests/runit.splitRaw.R
inst/unitTests/runit.stopOnError.R
inst/unitTests/runit.subset_extraction.R
inst/unitTests/runit.unusedGroups.R
inst/unitTests/runit.updateObject.R
inst/unitTests/runit.useOriginalCode.R
inst/unitTests/runit.writecdf.R
inst/unitTests/runit.writemzdata.R
inst/unitTests/runit.writemzquantml.R
inst/unitTests/runit.xcmsRawCopy.R
inst/unitTests/runit.xcmsSet.R
man
man/AutoLockMass-methods.Rd
man/Chromatogram-class.Rd
man/GenericParam.Rd
man/ProcessHistory-class.Rd
man/SSgauss.Rd
man/XCMSnExp-class.Rd
man/XCMSnExp-filter-methods.Rd
man/XCMSnExp-inherited-methods.Rd
man/XCMSnExp-peak-grouping-results.Rd
man/absent-methods.Rd
man/adjustRtime-obiwarp.Rd
man/adjustRtime-peakGroups.Rd
man/adjustRtime.Rd
man/binYonX.Rd
man/breaks_on_binSize.Rd
man/breaks_on_nBins.Rd
man/c.xcmsSet.Rd
man/calibrate.Rd
man/chromatographic-peak-detection.Rd
man/colMax.Rd
man/collect-methods.Rd
man/descendZero.Rd
man/diffreport-methods.Rd
man/do_adjustRtime_peakGroups.Rd
man/do_findChromPeaks_centWave.Rd
man/do_findChromPeaks_centWaveWithPredIsoROIs.Rd
man/do_findChromPeaks_massifquant.Rd
man/do_findChromPeaks_matchedFilter.Rd
man/do_findPeaks_MSW.Rd
man/do_groupChromPeaks_density.Rd
man/do_groupChromPeaks_nearest.Rd
man/do_groupPeaks_mzClust.Rd
man/doubleMatrix.Rd
man/etg.Rd
man/extractChromatograms-method.Rd
man/fillChromPeaks.Rd
man/fillPeaks-methods.Rd
man/fillPeaks.MSW-methods.Rd
man/fillPeaks.chrom-methods.Rd
man/filtfft.Rd
man/findChromPeaks-centWave.Rd
man/findChromPeaks-centWaveWithPredIsoROIs.Rd
man/findChromPeaks-massifquant.Rd
man/findChromPeaks-matchedFilter.Rd
man/findEqualGreater.Rd
man/findMZ.Rd
man/findPeaks-MSW.Rd
man/findPeaks-methods.Rd
man/findPeaks.MS1-methods.Rd
man/findPeaks.MSW-xcmsRaw-method.Rd
man/findPeaks.addPredictedIsotopeFeatures-methods.Rd
man/findPeaks.centWave-methods.Rd
man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd
man/findPeaks.massifquant-methods.Rd
man/findPeaks.matchedFilter-xcmsRaw-method.Rd
man/findneutral.Rd
man/getEIC-methods.Rd
man/getPeaks-methods.Rd
man/getScan-methods.Rd
man/getSpec-methods.Rd
man/getXcmsRaw-methods.Rd
man/group-methods.Rd
man/group.density.Rd
man/group.mzClust.Rd
man/group.nearest.Rd
man/groupChromPeaks-density.Rd
man/groupChromPeaks-mzClust.Rd
man/groupChromPeaks-nearest.Rd
man/groupChromPeaks.Rd
man/groupnames-methods.Rd
man/groupval-methods.Rd
man/image.xcmsRaw.Rd
man/imputeLinInterpol.Rd
man/levelplot.xcmsRaw.Rd
man/loadRaw-methods.Rd
man/medianFilter.Rd
man/msn2xcmsRaw.Rd
man/na.flatfill.Rd
man/panel.cor.Rd
man/peakPlots-methods.Rd
man/peakTable-methods.Rd
man/plot.xcmsEIC.Rd
man/plotAdjustedRtime.Rd
man/plotChrom-methods.Rd
man/plotEIC-methods.Rd
man/plotPeaks-methods.Rd
man/plotQC.Rd
man/plotRaw-methods.Rd
man/plotScan-methods.Rd
man/plotSpec-methods.Rd
man/plotSurf-methods.Rd
man/plotTIC-methods.Rd
man/plotrt-methods.Rd
man/profGenerate.Rd
man/profMat-xcmsSet.Rd
man/profMedFilt-methods.Rd
man/profMethod-methods.Rd
man/profRange-methods.Rd
man/profStep-methods.Rd
man/pval.Rd
man/rawEIC-methods.Rd
man/rawMat-methods.Rd
man/rectUnique.Rd
man/retcor-methods.Rd
man/retcor.obiwarp-methods.Rd
man/retcor.peakgroups-methods.Rd
man/retexp.Rd
man/sampnames-methods.Rd
man/showError-xcmsSet-method.Rd
man/specDist-methods.Rd
man/specDist.cosine-methods.Rd
man/specDist.meanMZmatch-methods.Rd
man/specDist.peakCount-methods.Rd
man/specNoise.Rd
man/specPeaks.Rd
man/split.xcmsRaw.Rd
man/split.xcmsSet.Rd
man/stitch-methods.Rd
man/sub-xcmsRaw-logicalOrNumeric-missing-missing-method.Rd
man/updateObject-xcmsSet-method.Rd
man/useOriginalCode.Rd
man/verify.mzQuantML.Rd
man/write.cdf-methods.Rd
man/write.mzQuantML.Rd
man/write.mzdata-methods.Rd
man/writeMzTab.Rd
man/xcms-deprecated.Rd
man/xcmsEIC-class.Rd
man/xcmsFileSource-class.Rd
man/xcmsFragments-class.Rd
man/xcmsFragments.Rd
man/xcmsPapply.Rd
man/xcmsPeaks-class.Rd
man/xcmsRaw-class.Rd
man/xcmsRaw.Rd
man/xcmsSet-class.Rd
man/xcmsSet.Rd
man/xcmsSource-class.Rd
man/xcmsSource-methods.Rd
readme.org
src
src/Makevars
src/Makevars.win
src/binarySearch.h
src/binners.c
src/binners.h
src/fastMatch.c
src/massifquant
src/massifquant/DataKeeper.cpp
src/massifquant/DataKeeper.h
src/massifquant/OpOverload.cpp
src/massifquant/OpOverload.h
src/massifquant/SegProc.cpp
src/massifquant/SegProc.h
src/massifquant/TrMgr.cpp
src/massifquant/TrMgr.h
src/massifquant/Tracker.cpp
src/massifquant/Tracker.h
src/massifquant/dpq.h
src/massifquant/nmath.h
src/massifquant/xcms_massifquant.cpp
src/mzClust_hclust.c
src/mzROI.c
src/obiwarp
src/obiwarp/lmat.h
src/obiwarp/mat.cpp
src/obiwarp/mat.h
src/obiwarp/vec.cpp
src/obiwarp/vec.h
src/obiwarp/xcms_dynprog.cpp
src/obiwarp/xcms_dynprog.h
src/obiwarp/xcms_lmat.cpp
src/util.c
src/util.h
src/win
src/win/i386
src/win/x64
src/xcms.c
src/xcms.h
src/xcms_obiwarp.cpp
tests
tests/doRUnit.R
vignettes
vignettes/FlowChart.graffle
vignettes/FlowChart.pdf
vignettes/benchmarking.Rmd-notrun
vignettes/biomed-central.csl
vignettes/new_functionality.Rmd
vignettes/new_functionality.org
vignettes/references.bib
vignettes/xcms.bib
vignettes/xcms.org
vignettes/xcmsDirect.Rnw
vignettes/xcmsInstall.Rnw
vignettes/xcmsMSn.Rnw
vignettes/xcmsPreprocess.Rnw
xcms documentation built on May 20, 2017, 10:51 p.m.