xcms
LC-MS and GC-MS Data Analysis

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Source code
102
Man pages
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xcms: LC-MS and GC-MS Data Analysis
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API

API for xcms
LC-MS and GC-MS Data Analysis

Global functions
$,xcmsSet-method Man page
$<-,xcmsSet-method Man page
.MSW_orig Source code Source code
.XCMSnExp2SummarizedExperiment Source code
.XCMSnExp2xcmsSet Source code
.add_chromatogram_peaks Source code
.adjust_with_linear_model Source code
.aggregateMethod2int Source code
.align_chromatogram Source code
.align_chromatogram_approx Source code
.align_chromatogram_match_rtime Source code
.applyRtAdjToChromPeaks Source code
.applyRtAdjustment Source code
.calibrate_mz Source code
.centWave_new Source code
.centWave_orig Source code
.chrom_merge_neighboring_peaks Source code
.chrom_peak_data Source code
.chrom_peaks_above_threshold Source code
.concatenate_OnDiskMSnExp Source code
.concatenate_XCMSnExp Source code
.copy_env Source code
.correlate_chromatogram Source code
.correlate_chromatograms Source code
.correlate_chromatograms_self Source code
.createProfileMatrix Source code
.estimate_prec_intensity Source code
.extractMsData Source code
.featureIDs Source code
.feature_values Source code
.features_ms_region Source code
.filterChromPeaks Source code
.filter_file_XCMSnExp Source code
.findChromPeaks_XChromatograms Source code
.fix_mz_clust_peaks Source code
.getChromPeakData Source code
.getChromPeakData_matchedFilter Source code
.getMSWPeakData Source code
.getMSWPeakData2 Source code
.getPeakGroupsRtMatrix Source code
.getPeaks_new Source code
.getPeaks_orig Source code
.getProcessErrors Source code
.getProcessHistory Source code
.getRtROI Source code
.get_closest_index Source code
.group_overlapping_peaks Source code
.group_peaks_density Source code
.hasFilledPeaks Source code
.has_chrom_peak_data Source code
.impute2method Source code
.imputeMethod2int Source code
.insertColumn Source code
.match_closest Source code
.match_trim_vector_index Source code
.match_trim_vectors Source code
.matchedFilter_binYonX_no_iter Source code
.matchedFilter_orig Source code
.matchpeaks2 Source code
.merge_neighboring_peaks Source code
.method Source code
.mz Source code
.mzabs Source code
.mzppm Source code
.narrow_rt_boundaries Source code
.neighbors Source code
.normalize_chromatogram Source code
.obiwarp Source code
.onAttach Source code
.onLoad Source code
.onUnload Source code
.pSet2xcmsSet Source code
.param2list Source code
.param2string Source code
.peakIndex Source code
.peaks_to_result Source code
.plotChromPeakDensity Source code
.plot_XIC Source code
.plot_chrom_peak_density Source code
.ppm Source code
.ppm_range Source code
.processResultList Source code
.process_history_subset_samples Source code
.rawMat Source code
.rbind_fill Source code
.reconstruct_ms2_for_chrom_peak Source code
.reconstruct_ms2_for_peaks_file Source code
.rect_overlap Source code
.reduce Source code
.retcor.peakgroups_orig Source code
.setXCMSOptions Source code
.split_by_file Source code
.split_by_file2 Source code
.subset_chrom_peaks_xchromatograms Source code
.subset_features_on_chrom_peaks Source code
.swath_collect_chrom_peaks Source code
.update_feature_definitions Source code
.validChromPeakData Source code
.validChromPeaksMatrix Source code
.validProcessHistory Source code
.validXChromatogram Source code
.validXChromatograms Source code
.which_chrom_peak_diff_rt Source code
.which_chrom_peak_overlap_rt Source code
.which_mz_in_range Source code
.write.metaboanalyst Source code
.xchrom_merge_neighboring_peaks Source code
.xcmsFragments.collect Source code
.xcmsFragments.hasMSn Source code
.xcmsFragments.plotTree Source code
.xcmsFragments.show Source code
AutoLockMass Man page
AutoLockMass,xcmsRaw-method Man page
AutoLockMass-methods Man page
CalibrantMassParam Man page Source code
CalibrantMassParam-class Man page
CentWaveParam Man page Source code
CentWaveParam-class Man page
CentWavePredIsoParam Man page Source code
CentWavePredIsoParam-class Man page
ChromPeakAreaParam Man page Source code
ChromPeakAreaParam-class Man page
CleanPeaksParam Man page Source code
CleanPeaksParam-class Man page
FillChromPeaksParam Man page Source code
FillChromPeaksParam-class Man page
FilterIntensityParam Man page Source code
FilterIntensityParam-class Man page
GenericParam Man page Source code
GenericParam-class Man page
GenericProcessHistory Source code
MSW Man page
MSW.extendLength Source code
MSW.extendNBase Source code
MSW.getLocalMaximumCWT Source code
MSW.getRidge Source code
MSWParam Man page Source code
MSWParam-class Man page
MassifquantParam Man page Source code
MassifquantParam-class Man page
MatchedFilterParam Man page Source code
MatchedFilterParam-class Man page
MergeNeighboringPeaksParam Man page Source code
MergeNeighboringPeaksParam-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
Param Man page
Param-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
XCMSnExp-filter Man page
XChromatogram Man page Source code
XChromatogram-class Man page
XChromatograms Man page Source code
XChromatograms-class Man page
XProcessHistory Man page Source code
XProcessHistory-class Man page
[,XCMSnExp,ANY,ANY,ANY-method Man page
[,XChromatograms,ANY,ANY,ANY-method Man page
[,xcmsRaw,logicalOrNumeric,missing,missing-method Man page
[,xcmsSet,ANY,ANY,ANY-method Man page
[,xcmsSet-method Man page
[[,XCMSnExp,ANY,ANY-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
adjustRtimeSubset Source code
adjustWithModel 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
align Man page
align,Chromatogram,Chromatogram-method Man page
align,MChromatograms,Chromatogram-method Man page
ampTh Man page
ampTh,MSWParam-method Man page
ampTh<- Man page
ampTh<-,MSWParam-method Man page
applyAdjustedRtime Man page Source code
applyModelAdjustment Source code
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.XCMSnExp Man page Source code
c.xcmsSet Man page Source code
calibrate Man page
calibrate,XCMSnExp-method Man page
calibrate,xcmsSet-method Man page
cent Source code
centWave Man page
centWaveWithPredIsoROIs Man page
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
chromPeakData Man page
chromPeakData,MsFeatureData-method Man page
chromPeakData,XCMSnExp-method Man page
chromPeakData,XChromatogram-method Man page
chromPeakData,XChromatograms-method Man page
chromPeakData<- Man page
chromPeakData<-,MsFeatureData-method Man page
chromPeakData<-,XCMSnExp-method Man page
chromPeakData<-,XChromatogram-method Man page
chromPeakSpectra Man page Source code
chromPeaks Man page
chromPeaks,MsFeatureData-method Man page
chromPeaks,XCMSnExp-method Man page
chromPeaks,XChromatogram-method Man page
chromPeaks,XChromatograms-method Man page
chromPeaks<- Man page
chromPeaks<-,MsFeatureData-method Man page
chromPeaks<-,XCMSnExp-method Man page
chromPeaks<-,XChromatogram-method Man page
chromatogram Man page
chromatogram,XCMSnExp-method Man page
chromatographic-peak-detection Man page
class:Param Man page
clean,XCMSnExp-method Man page
coerce,MChromatograms,XChromatograms-method Man page
colMax Man page
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
correlate Man page
correlate,Chromatogram,Chromatogram-method Man page
correlate,MChromatograms,MChromatograms-method Man page
correlate,MChromatograms,missing-method Man page
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
dirname Man page
dirname,OnDiskMSnExp-method Man page
dirname<-,OnDiskMSnExp-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_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
dropFeatureDefinitions,XChromatograms-method Man page
dropFilledChromPeaks Man page
dropFilledChromPeaks,XCMSnExp-method Man page
dropFilledChromPeaks,XChromatogram-method Man page
dropFilledChromPeaks,XChromatograms-method Man page
dropGenericProcessHistory Source code
dropGenericProcessHistoryList Source code
dropProcessHistories Source code
dropProcessHistoriesList Source code
estimate Source code
estimateChromNoise Source code
estimatePrecursorIntensity Man page 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
exportMetaboAnalyst Man page Source code
extraPeaks Man page
extraPeaks,PeakGroupsParam-method Man page
extraPeaks<- Man page
extraPeaks<-,PeakGroupsParam-method Man page
extractMsData Man page
extractMsData,OnDiskMSnExp-method Man page
extractMsData,XCMSnExp-method Man page
faahko_sub Man page
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
featureChromatograms Man page Source code
featureDefinitions Man page
featureDefinitions,MsFeatureData-method Man page
featureDefinitions,XCMSnExp-method Man page
featureDefinitions,XChromatograms-method Man page
featureDefinitions<- Man page
featureDefinitions<-,MsFeatureData-method Man page
featureDefinitions<-,XCMSnExp-method Man page
featureSpectra Man page Source code
featureSummary Man page Source code
featureValues Man page
featureValues,XCMSnExp-method Man page
featureValues,XChromatograms-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,ChromPeakAreaParam-method 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
filterColumnsIntensityAbove Man page
filterColumnsIntensityAbove,MChromatograms-method Man page
filterColumnsIntensityAbove,XChromatograms-method Man page
filterColumnsKeepTop Man page
filterColumnsKeepTop,MChromatograms-method Man page
filterColumnsKeepTop,XChromatograms-method Man page
filterFeatureDefinitions Man page Source code
filterFile,XCMSnExp-method Man page
filterMsLevel,XCMSnExp-method Man page
filterMz,XCMSnExp-method Man page
filterMz,XChromatogram-method Man page
filterMz,XChromatograms-method Man page
filterRt,XCMSnExp-method Man page
filterRt,XChromatogram-method Man page
filterRt,XChromatograms-method Man page
filtfft Man page Source code
findChromPeaks Man page
findChromPeaks,Chromatogram,CentWaveParam-method Man page
findChromPeaks,Chromatogram,MatchedFilterParam-method Man page
findChromPeaks,MChromatograms,CentWaveParam-method Man page
findChromPeaks,MChromatograms,MatchedFilterParam-method 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,Param-method Man page
findChromPeaks-Chromatogram-CentWaveParam Man page
findChromPeaks-centWave Man page
findChromPeaks-centWaveWithPredIsoROIs Man page
findChromPeaks-massifquant Man page
findChromPeaks-matchedFilter Man page
findChromPeaksInFile Source code
findChromPeaksIsolationWindow Man page 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
fixedMz Man page Source code
fixedRt Man page Source code
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
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
getMsnScan Man page
getMsnScan,xcmsRaw-method Man page
getPeaks Man page
getPeaks,xcmsRaw-method Man page
getPeaks-methods Man page
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,XChromatograms,PeakDensityParam-method Man page
groupChromPeaks-density Man page
groupChromPeaks-mzClust Man page
groupChromPeaks-nearest Man page
groupOverlaps Man page Source code
groupidx Man page
groupidx,xcmsSet-method Man page
groupidx<- Man page
groupidx<-,xcmsSet-method Man page
groupnames Man page
groupnames,XCMSnExp-method 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,OnDiskMSnExp-method Man page
hasAdjustedRtime,XCMSnExp-method Man page
hasChromPeaks Man page
hasChromPeaks,MsFeatureData-method Man page
hasChromPeaks,XCMSnExp-method Man page
hasChromPeaks,XChromatogram-method Man page
hasChromPeaks,XChromatograms-method Man page
hasFeatures Man page
hasFeatures,MsFeatureData-method Man page
hasFeatures,XCMSnExp-method Man page
hasFeatures,XChromatograms-method Man page
hasFilledChromPeaks Man page Source code
hasFilledChromPeaks,XCMSnExp-method Man page
hasFilledChromPeaks,XChromatograms-method Man page
highlightChromPeaks Man page 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
imputeRowMin Man page Source code
imputeRowMinRand 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,XCMSnExp-method Man page
isCalibrated Man page Source code
isolationWindowTargetMz Man page
isolationWindowTargetMz,OnDiskMSnExp-method Man page
joinOverlappingPeaks Source code
kNN Man page
kNN,NearestPeaksParam-method Man page
kNN<- Man page
kNN<-,NearestPeaksParam-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
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
ms2_spectra_for_all_peaks Source code
ms2_spectra_for_features Source code
ms2_spectra_for_peaks_from_file Source code
msLevel,XProcessHistory-method Man page
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,CalibrantMassParam 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
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,Chromatogram-method Man page
normalize,MChromatograms-method Man page
normalize,XCMSnExp-method Man page
normalize-Chromatogram Man page
overlappingFeatures Man page Source code
panel.cor Man page Source code
patternVsRowScore Source code
peakGroupsMatrix Man page
peakGroupsMatrix,PeakGroupsParam-method Man page
peakGroupsMatrix<- Man page
peakGroupsMatrix<-,PeakGroupsParam-method Man page
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
peaksWithCentWave Man page Source code
peaksWithMatchedFilter Man page Source code
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 Man page Source code
pickPeaks,XCMSnExp-method Man page
plot, plot-methods Man page
plot,XCMSnExp,missing-method Man page
plot,XChromatogram,ANY-method Man page
plot,XChromatograms,ANY-method 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
plotChromPeakDensity Man page
plotChromPeakDensity,XCMSnExp-method Man page
plotChromPeakDensity,XChromatograms-method Man page
plotChromPeakImage Man page Source code
plotChromPeaks Man page Source code
plotEIC Man page
plotEIC,xcmsRaw-method Man page
plotMsData Man page Source code
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
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
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
processHistory,XChromatograms-method Man page
processHistoryTypes Man page Source code
processInfo Man page
processInfo,ProcessHistory-method Man page
processParam Man page
processParam,XProcessHistory-method Man page
processType Man page
processType,ProcessHistory-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
quantify,XCMSnExp-method Man page
rawEIC Man page
rawEIC,xcmsRaw-method Man page
rawMat Man page
rawMat,xcmsRaw-method Man page
rawMat-methods Man page
rbind.ragged Source code
read.mascot Source code
readRawData Source code
reconstructChromPeakSpectra Man page Source code
rectUnique Man page Source code
refineChromPeaks Man page
refineChromPeaks,XCMSnExp,CleanPeaksParam-method Man page
refineChromPeaks,XCMSnExp,FilterIntensityParam-method Man page
refineChromPeaks,XCMSnExp,MergeNeighboringPeaksParam-method Man page
refineChromPeaks,XChromatogram,MergeNeighboringPeaksParam-method Man page
refineChromPeaks,XChromatograms,MergeNeighboringPeaksParam-metho Man page
remakeTIC Source code
removeIntensity Man page
removeIntensity,Chromatogram-method Man page
removeIntensity,MChromatograms-method Man page
removeIntensity,XChromatogram-method Man page
removePeaks,XCMSnExp-method Man page
replaceNaOnEnds Source code
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
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
rla Man page Source code
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
rowFitModel Source code
rowMax Man page
rowRla Man page Source code
rtime,XCMSnExp-method Man page
rtrange Man page
rtrange,xcmsEIC-method Man page
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
show,CentWaveParam-method Man page
show,CentWavePredIsoParam-method Man page
show,CleanPeaksParam-method Man page
show,FillChromPeaksParam-method Man page
show,FilterIntensityParam-method Man page
show,GenericParam-method Man page
show,MSWParam-method Man page
show,MassifquantParam-method Man page
show,MatchedFilterParam-method Man page
show,MergeNeighboringPeaksParam-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,XChromatogram-method Man page
show,XChromatograms-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
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
spectrapply,XCMSnExp-method Man page
split, split-methods Man page
split,XCMSnExp,ANY-method 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 Man page
subset,ObiwarpParam-method Man page
subset,PeakGroupsParam-method Man page
subset-xcmsRaw Man page
subset<- Man page
subset<-,ObiwarpParam-method Man page
subset<-,PeakGroupsParam-method Man page
subsetAdjust Man page
subsetAdjust,ObiwarpParam-method Man page
subsetAdjust,PeakGroupsParam-method Man page
subsetAdjust<- Man page
subsetAdjust<-,ObiwarpParam-method Man page
subsetAdjust<-,PeakGroupsParam-method 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,XCMSnExp-method Man page
updateObject,xcmsSet-method Man page
useOriginalCode Man page 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
weightedMeanAroundApex Source code
which.colMax Man page
which.rowMax Man page
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.mzQuantML Man page
write.mzQuantML,xcmsSet-method Man page
write.mzdata Man page
write.mzdata,xcmsRaw-method Man page
writeMSData,XCMSnExp,character-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.makeXS Source code
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
xcms documentation built on Nov. 8, 2020, 5:13 p.m.

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