Package: xcms 4.5.0
Steffen Neumann
xcms: LC-MS and GC-MS Data Analysis
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.
Authors:
xcms_4.5.0.tar.gz
xcms_4.5.0.zip(r-4.5)xcms_4.5.0.zip(r-4.4)xcms_4.5.0.zip(r-4.3)
xcms_4.5.0.tgz(r-4.4-x86_64)xcms_4.5.0.tgz(r-4.4-arm64)xcms_4.5.0.tgz(r-4.3-x86_64)xcms_4.5.0.tgz(r-4.3-arm64)
xcms_4.5.0.tar.gz(r-4.5-noble)xcms_4.5.0.tar.gz(r-4.4-noble)
xcms_4.5.0.tgz(r-4.4-emscripten)xcms_4.5.0.tgz(r-4.3-emscripten)
xcms.pdf |xcms.html✨
xcms/json (API)
NEWS
| # Install 'xcms' in R: |
| install.packages('xcms', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sneumann/xcms/issues
Datasets:
- faahko_sub - LC-MS preprocessing result test data sets
- faahko_sub2 - LC-MS preprocessing result test data sets
- xdata - LC-MS preprocessing result test data sets
- xmse - LC-MS preprocessing result test data sets
On BioConductor:xcms-4.5.0(bioc 3.21)xcms-4.4.0(bioc 3.20)
immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detection
Last updated 20 days agofrom:3c1702c2cc. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 31 2024 |
Exports:absentabsMzabsMz<-absRtabsRt<-addParamsaddParams<-adjustedRtimeadjustedRtime<-adjustRtimeadjustRtimePeakGroupsampThampTh<-applyAdjustedRtimeAutoLockMassbaseValuebaseValue<-binbinSizebinSize<-binYonXBlankFlagbreaks_on_binSizebreaks_on_nBinsbwbw<-CalibrantMassParamcalibratecenterSamplecenterSample<-CentWaveParamCentWavePredIsoParamcheckBackcheckBack<-chromatogramChromPeakAreaParamchromPeakChromatogramschromPeakDatachromPeakData<-chromPeakschromPeaks<-chromPeakSpectracleanCleanPeaksParamcollectconsecMissedLimitconsecMissedLimit<-correlatecriticalValuecriticalValue<-deepCopydiffreportdirnamedirname<-distancedistance<-distFundistFun<-do_adjustRtime_peakGroupsdo_findChromPeaks_addPredIsoROIsdo_findChromPeaks_centWavedo_findChromPeaks_centWaveWithPredIsoROIsdo_findChromPeaks_massifquantdo_findChromPeaks_matchedFilterdo_findPeaks_MSWdo_groupChromPeaks_densitydo_groupChromPeaks_nearestdo_groupPeaks_mzClustDratioFilterdropAdjustedRtimedropChromPeaksdropFeatureDefinitionsdropFilledChromPeaksEicSimilarityParamestimatePrecursorIntensityetgexpandMzexpandMz<-expandRtexpandRt<-exportMetaboAnalystextractMsDataextraPeaksextraPeaks<-factorDiagfactorDiag<-factorGapfactorGap<-familyfamily<-featureAreafeatureChromatogramsfeatureDefinitionsfeatureDefinitions<-featureGroupsfeatureGroups<-featureSpectrafeatureSummaryfeatureValuesfileIndexfileNamesfilepathsfilepaths<-fillChromPeaksFillChromPeaksParamfillPeaksfillPeaks.chromfillPeaks.MSWfilterAcquisitionNumfilterChromPeaksfilterColumnsIntensityAbovefilterColumnsKeepTopfilterFeatureDefinitionsfilterFileFilterIntensityParamfilterMsLevelfilterMzfilterMzRangefilterRtfindChromPeaksfindChromPeaksIsolationWindowfindMZfindmzROIfindneutralfindPeaksfindPeaks.addPredictedIsotopeFeaturesfindPeaks.centWavefindPeaks.centWaveWithPredictedIsotopeROIsfindPeaks.massifquantfindPeaks.matchedFilterfindPeaks.MSWfirstBaselineCheckfirstBaselineCheck<-fitgaussfitgauss<-fixedMzfixedRtfromFilefwhmfwhm<-gapExtendgapExtend<-gapInitgapInit<-GenericParamgetEICgetMsnScangetPeaksgetScangetSpecgetXcmsRawgroupgroup.densitygroup.mzClustgroup.nearestgroupChromPeaksgroupidxgroupidx<-groupnamesgroupOverlapsgroupsgroups<-groupvalhasAdjustedRtimehasChromPeakshasFeatureshasFilledChromPeakshighlightChromPeaksimageimputeimpute<-imputeLinInterpolimputeRowMinimputeRowMinRandindexindex<-initPenaltyinitPenalty<-integrateintegrate<-intensityisCalibratedisolationWindowTargetMzkNNkNN<-LamaParamalevelplotloadRawloadXcmsDatalocalAlignmentlocalAlignment<-manualChromPeaksmanualFeaturesMassifquantParamMatchedFilterParammatchedRtimesmatchLamasChromPeaksmax<-maxChargemaxCharge<-maxFeaturesmaxFeatures<-maxIsomaxIso<-medianFilterMergeNeighboringPeaksParamminFractionminFraction<-minNoiseLevelminNoiseLevel<-minSamplesminSamples<-mslevelmsn2xcmsRawMSWParammzmzCenterFunmzCenterFun<-MzClustParammzdiffmzdiff<-mzIntervalExtensionmzIntervalExtension<-mzrangemzVsRtBalancemzVsRtBalance<-nearbyPeaknearbyPeak<-NearestPeaksParamnoisenoise<-ObiwarpParamoverlappingFeaturesPeakDensityParampeakGroupsMatrixpeakGroupsMatrix<-PeakGroupsParampeakspeaks<-peakScaleRangepeakScaleRange<-peaksWithCentWavepeaksWithMatchedFilterpeakTablepeakThrpeakThr<-peakwidthpeakwidth<-PercentMissingFilterphenoDataphenoData<-phenoDataFromPathspickPeaksplotplotAdjustedRtimeplotChromplotChromatogramsOverlayplotChromPeakDensityplotChromPeakImageplotChromPeaksplotEICplotFeatureGroupsplotMsDataplotPeaksplotPrecursorIonsplotQCplotRawplotrtplotScanplotSpecplotSurfplotTICplotTreepolaritypolarity<-ppmppm<-prefilterprefilter<-presentprocessDateprocessHistoryprocessHistoryTypesprocessInfoprocessParamprocessTypeprofinfoprofinfo<-profMatprofMedFiltprofMethodprofMethod<-profMzprofRangeprofStepprofStep<-progressCallbackprogressCallback<-quantifyrawEICrawMatreconstructChromPeakSpectrarefineChromPeaksremoveIntensityremovePeaksresponseresponse<-retcorretcor.obiwarpretcor.peakgroupsretexprevMzridgeLengthridgeLength<-rlaroiListroiList<-roiScalesrowRlaRsdFilterrtimertrangesampclasssampclass<-sampleGroupssampleGroups<-sampnamessampnames<-scalesscales<-scanrangesetAsshowshowErrorsigmasigma<-smoothsmooth<-snthreshsnthresh<-snthreshIsoROIssnthreshIsoROIs<-sortMzspanspan<-specDistspecDist.cosinespecDist.meanMZmatchspecDist.peakCountspecNoisespecPeaksspectraspectrapplysplitSSgaussstepssteps<-stitchsubsetsubset<-subsetAdjustsubsetAdjust<-summarizeLamaMatchtransformIntensitytuneIntuneIn<-unionsunions<-uniqueMsLevelsupdateObjectuseOriginalCodeverboseColumnsverboseColumns<-verify.mzQuantMLwithWavewithWave<-write.cdfwrite.mzdatawrite.mzQuantMLwriteMSDataXChromatogramXChromatogramsXcmsExperimentxcmsFragmentsxcmsRawxcmsSetxcmsSource
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryamlzlibbioc
Grouping FTICR-MS data with xcms
Rendered fromxcms-direct-injection.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-03-13
Started: 2017-08-09
LC-MS data preprocessing and analysis with xcms
Rendered fromxcms.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-04-04
Started: 2017-09-29
Compounding (grouping) of LC-MS features
Rendered fromLC-MS-feature-grouping.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-03-13
Started: 2021-08-03
LC-MS/MS data analysis with xcms
Rendered fromxcms-lcms-ms.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-08-09
Started: 2019-10-04
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| XCMSnExp filtering and subsetting | filterChromPeaks,XCMSnExp-method filterFeatureDefinitions,XCMSnExp-method filterFile,XCMSnExp-method filterMsLevel,XCMSnExp-method filterMz,XCMSnExp-method filterRt,XCMSnExp-method split,XCMSnExp,ANY-method XCMSnExp-filter [,XCMSnExp,ANY,ANY,ANY-method [[,XCMSnExp,ANY,ANY-method |
| Subset an xcmsRaw object by scans | subset-xcmsRaw [,xcmsRaw,logicalOrNumeric,missing,missing-method |
| Determine which peaks are absent / present in a sample class | absent absent,xcmsSet-method present present,xcmsSet-method |
| Alignment: Retention time correction methods. | adjustRtime adjustRtime,MsExperiment,ObiwarpParam-method adjustRtime,MsExperiment,PeakGroupsParam-method adjustRtime,OnDiskMSnExp,ObiwarpParam-method adjustRtime,XCMSnExp,ObiwarpParam-method adjustRtime,XCMSnExp,PeakGroupsParam-method adjustRtimePeakGroups binSize,ObiwarpParam-method binSize<-,ObiwarpParam-method centerSample centerSample,ObiwarpParam-method centerSample<- centerSample<-,ObiwarpParam-method distFun distFun,ObiwarpParam-method distFun<- distFun<-,ObiwarpParam-method extraPeaks extraPeaks,PeakGroupsParam-method extraPeaks<- extraPeaks<-,PeakGroupsParam-method factorDiag factorDiag,ObiwarpParam-method factorDiag<- factorDiag<-,ObiwarpParam-method factorGap factorGap,ObiwarpParam-method factorGap<- factorGap<-,ObiwarpParam-method family family,PeakGroupsParam-method family<- family<-,PeakGroupsParam-method gapExtend gapExtend,ObiwarpParam-method gapExtend<- gapExtend<-,ObiwarpParam-method gapInit gapInit,ObiwarpParam-method gapInit<- gapInit<-,ObiwarpParam-method initPenalty initPenalty,ObiwarpParam-method initPenalty<- initPenalty<-,ObiwarpParam-method localAlignment localAlignment,ObiwarpParam-method localAlignment<- localAlignment<-,ObiwarpParam-method minFraction,PeakGroupsParam-method minFraction<-,PeakGroupsParam-method ObiwarpParam ObiwarpParam-class peakGroupsMatrix peakGroupsMatrix,PeakGroupsParam-method peakGroupsMatrix<- peakGroupsMatrix<-,PeakGroupsParam-method PeakGroupsParam PeakGroupsParam-class response response,ObiwarpParam-method response<- response<-,ObiwarpParam-method smooth smooth,PeakGroupsParam-method smooth<- smooth<-,PeakGroupsParam-method span span,PeakGroupsParam-method span<- span<-,PeakGroupsParam-method subset subset,ObiwarpParam-method subset,PeakGroupsParam-method subset<- subset<-,ObiwarpParam-method subset<-,PeakGroupsParam-method subsetAdjust subsetAdjust,ObiwarpParam-method subsetAdjust,PeakGroupsParam-method subsetAdjust<- subsetAdjust<-,ObiwarpParam-method subsetAdjust<-,PeakGroupsParam-method |
| Landmark-based alignment: aligning a dataset against an external reference | adjustRtime,XcmsExperiment,LamaParama-method LamaParama LamaParama-class matchedRtimes matchLamasChromPeaks plot,LamaParama,ANY-method summarizeLamaMatch |
| Replace raw with adjusted retention times | applyAdjustedRtime |
| Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ | AutoLockMass AutoLockMass,xcmsRaw-method AutoLockMass-methods |
| XCMSnExp data manipulation methods inherited from MSnbase | bin,XCMSnExp-method clean,XCMSnExp-method filterAcquisitionNum,XCMSnExp-method normalize,XCMSnExp-method pickPeaks,XCMSnExp-method removePeaks,XCMSnExp-method smooth,XCMSnExp-method |
| Aggregate values in y for bins defined on x | binYonX |
| Flag features based on the intensity in blank samples | BlankFlag filterFeatures,SummarizedExperiment,BlankFlag-method filterFeatures,XcmsResult,BlankFlag-method |
| Generate breaks for binning using a defined bin size. | breaks_on_binSize |
| Generate breaks for binning | breaks_on_nBins |
| Combine xcmsSet objects | c, c-methods c.xcmsSet |
| Calibrant mass based calibration of chromatgraphic peaks | CalibrantMassParam CalibrantMassParam-class calibrate,XCMSnExp-method isCalibrated mz,CalibrantMassParam |
| Calibrate peaks for correcting unprecise m/z values | calibrate calibrate,xcmsSet-method |
| Extracting chromatograms | chromatogram chromatogram,XCMSnExp-method |
| Extract an ion chromatogram for each chromatographic peak | chromPeakChromatograms chromPeakChromatograms,XcmsExperiment-method |
| Extract spectra associated with chromatographic peaks | chromPeakSpectra chromPeakSpectra,XcmsExperiment-method chromPeakSpectra,XCMSnExp-method |
| Collect MS^n peaks into xcmsFragments | collect collect,xcmsFragments-method collect,xcmsRaw-method collect-methods |
| Correlate chromatograms | correlate correlate,Chromatogram,Chromatogram-method correlate,MChromatograms,MChromatograms-method correlate,MChromatograms,missing-method |
| Create report of analyte differences | diffreport diffreport,xcmsSet-method |
| Change the file path of an 'OnDiskMSnExp' object | dirname dirname,OnDiskMSnExp-method dirname<-,OnDiskMSnExp-method |
| Align spectrum retention times across samples using peak groups found in most samples | do_adjustRtime_peakGroups |
| Core API function for centWave peak detection | do_findChromPeaks_centWave |
| Core API function for two-step centWave peak detection with isotopes | do_findChromPeaks_addPredIsoROIs do_findChromPeaks_centWaveWithPredIsoROIs |
| Core API function for massifquant peak detection | do_findChromPeaks_massifquant |
| Core API function for matchedFilter peak detection | do_findChromPeaks_matchedFilter |
| Core API function for single-spectrum non-chromatography MS data peak detection | do_findPeaks_MSW |
| Core API function for peak density based chromatographic peak grouping | do_groupChromPeaks_density |
| Core API function for chromatic peak grouping using a nearest neighbor approach | do_groupChromPeaks_nearest |
| Core API function for peak grouping using mzClust | do_groupPeaks_mzClust |
| Filter features based on the dispersion ratio | DratioFilter filterFeatures,SummarizedExperiment,DratioFilter-method filterFeatures,XcmsResult,DratioFilter-method |
| Estimate precursor intensity for MS level 2 spectra | estimatePrecursorIntensity,MsExperiment-method estimatePrecursorIntensity,OnDiskMSnExp-method |
| Empirically Transformed Gaussian function | etg |
| Export data for use in MetaboAnalyst | exportMetaboAnalyst |
| DEPRECATED: Extract a 'data.frame' containing MS data | extractMsData extractMsData,OnDiskMSnExp-method extractMsData,XCMSnExp-method |
| Compounding of LC-MS features | feature-grouping featureGroups,XcmsResult-method featureGroups<-,XcmsResult-method |
| Extract ion chromatograms for each feature | featureChromatograms featureChromatograms,XcmsExperiment-method featureChromatograms,XCMSnExp-method |
| Extract spectra associated with features | featureSpectra featureSpectra,XcmsExperiment-method featureSpectra,XCMSnExp-method |
| Simple feature summaries | featureSummary |
| Gap Filling | ChromPeakAreaParam ChromPeakAreaParam-class expandMz expandMz,FillChromPeaksParam-method expandMz<- expandMz<-,FillChromPeaksParam-method expandRt expandRt,FillChromPeaksParam-method expandRt<- expandRt<-,FillChromPeaksParam-method fillChromPeaks fillChromPeaks,XcmsExperiment,ChromPeakAreaParam-method fillChromPeaks,XCMSnExp,ChromPeakAreaParam-method fillChromPeaks,XCMSnExp,FillChromPeaksParam-method fillChromPeaks,XCMSnExp,missing-method FillChromPeaksParam FillChromPeaksParam-class fixedMz fixedRt ppm,FillChromPeaksParam-method ppm<-,FillChromPeaksParam-method |
| Integrate areas of missing peaks | fillPeaks fillPeaks,xcmsSet-method |
| Integrate areas of missing peaks | fillPeaks.chrom fillPeaks.chrom,xcmsSet-method |
| Integrate areas of missing peaks in FTICR-MS data | fillPeaks.MSW fillPeaks.MSW,xcmsSet-method |
| Filtering sets of chromatographic data | filterColumnsIntensityAbove filterColumnsIntensityAbove,MChromatograms-method filterColumnsIntensityAbove,XChromatograms-method filterColumnsKeepTop filterColumnsKeepTop,MChromatograms-method filterColumnsKeepTop,XChromatograms-method |
| Next Generation 'xcms' Result Object | adjustedRtime,XcmsExperiment-method chromatogram,MsExperiment-method chromatogram,XcmsExperiment-method chromPeakData,XcmsExperiment-method chromPeakData<-,XcmsExperiment-method chromPeaks,XcmsExperiment-method chromPeaks<-,XcmsExperiment-method dropAdjustedRtime,XcmsExperiment-method dropChromPeaks,XcmsExperiment-method dropFeatureDefinitions,XcmsExperiment-method dropFilledChromPeaks,XcmsExperiment-method featureArea featureDefinitions,XcmsExperiment-method featureDefinitions<-,XcmsExperiment-method featureValues,XcmsExperiment-method fileNames,MsExperiment-method filterChromPeaks filterChromPeaks,XcmsExperiment-method filterFeatureDefinitions filterFeatureDefinitions,XcmsExperiment-method filterFile,MsExperiment-method filterFile,XcmsExperiment-method filterIsolationWindow,MsExperiment-method filterIsolationWindow,XcmsExperiment-method filterMsLevel,MsExperiment-method filterMsLevel,XcmsExperiment-method filterMz,MsExperiment-method filterMzRange,MsExperiment-method filterMzRange,XcmsExperiment-method filterRt,MsExperiment-method filterRt,XcmsExperiment-method fromFile,MsExperiment-method hasAdjustedRtime,MsExperiment-method hasChromPeaks,XcmsExperiment-method hasFeatures,XcmsExperiment-method hasFilledChromPeaks,XcmsExperiment-method plot,MsExperiment,missing-method polarity,MsExperiment-method processHistory,XcmsExperiment-method quantify,XcmsExperiment-method rtime,MsExperiment-method rtime,XcmsExperiment-method show,XcmsExperiment-method uniqueMsLevels,MsExperiment-method XcmsExperiment XcmsExperiment-class [,XcmsExperiment,ANY,ANY,ANY-method |
| Filtering of features based on conventional quality assessment | filterFeatures |
| Chromatographic Peak Detection | findChromPeaks findChromPeaks,MsExperiment,Param-method findChromPeaks,XcmsExperiment,Param-method |
| Chromatographic peak detection using the centWave method | as.list,CentWaveParam-method centWave CentWaveParam CentWaveParam-class findChromPeaks,OnDiskMSnExp,CentWaveParam-method findChromPeaks-centWave firstBaselineCheck firstBaselineCheck,CentWaveParam-method firstBaselineCheck<- firstBaselineCheck<-,CentWaveParam-method fitgauss fitgauss,CentWaveParam-method fitgauss<- fitgauss<-,CentWaveParam-method integrate,CentWaveParam-method integrate<- integrate<-,CentWaveParam-method mzCenterFun mzCenterFun,CentWaveParam-method mzCenterFun<- mzCenterFun<-,CentWaveParam-method mzdiff mzdiff,CentWaveParam-method mzdiff<- mzdiff<-,CentWaveParam-method noise noise,CentWaveParam-method noise<- noise<-,CentWaveParam-method peakwidth peakwidth,CentWaveParam-method peakwidth<- peakwidth<-,CentWaveParam-method ppm ppm,CentWaveParam-method ppm<- ppm<-,CentWaveParam-method prefilter prefilter,CentWaveParam-method prefilter<- prefilter<-,CentWaveParam-method roiList roiList,CentWaveParam-method roiList<- roiList<-,CentWaveParam-method roiScales roiScales,CentWaveParam-method roiScales<- roiScales<-,CentWaveParam-method snthresh snthresh,CentWaveParam-method snthresh<- snthresh<-,CentWaveParam-method verboseColumns verboseColumns,CentWaveParam-method verboseColumns<- verboseColumns<-,CentWaveParam-method |
| Two-step centWave peak detection considering also isotopes | CentWavePredIsoParam CentWavePredIsoParam-class centWaveWithPredIsoROIs findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam-method findChromPeaks-centWaveWithPredIsoROIs maxCharge maxCharge,CentWavePredIsoParam-method maxCharge<- maxCharge<-,CentWavePredIsoParam-method maxIso maxIso,CentWavePredIsoParam-method maxIso<- maxIso<-,CentWavePredIsoParam-method mzIntervalExtension mzIntervalExtension,CentWavePredIsoParam-method mzIntervalExtension<- mzIntervalExtension<-,CentWavePredIsoParam-method polarity,CentWavePredIsoParam-method polarity<- polarity<-,CentWavePredIsoParam-method snthreshIsoROIs snthreshIsoROIs,CentWavePredIsoParam-method snthreshIsoROIs<- snthreshIsoROIs<-,CentWavePredIsoParam-method |
| Chromatographic peak detection using the massifquant method | checkBack checkBack,MassifquantParam-method checkBack<- checkBack<-,MassifquantParam-method consecMissedLimit consecMissedLimit,MassifquantParam-method consecMissedLimit<- consecMissedLimit<-,MassifquantParam-method criticalValue criticalValue,MassifquantParam-method criticalValue<- criticalValue<-,MassifquantParam-method findChromPeaks,OnDiskMSnExp,MassifquantParam-method findChromPeaks-massifquant fitgauss,MassifquantParam-method fitgauss<-,MassifquantParam-method integrate,MassifquantParam-method integrate<-,MassifquantParam-method massifquant MassifquantParam MassifquantParam-class mzCenterFun,MassifquantParam-method mzCenterFun<-,MassifquantParam-method mzdiff,MassifquantParam-method mzdiff<-,MassifquantParam-method noise,MassifquantParam-method noise<-,MassifquantParam-method peakwidth,MassifquantParam-method peakwidth<-,MassifquantParam-method ppm,MassifquantParam-method ppm<-,MassifquantParam-method prefilter,MassifquantParam-method prefilter<-,MassifquantParam-method snthresh,MassifquantParam-method snthresh<-,MassifquantParam-method unions unions,MassifquantParam-method unions<- unions<-,MassifquantParam-method verboseColumns,MassifquantParam-method verboseColumns<-,MassifquantParam-method withWave withWave,MassifquantParam-method withWave<- withWave<-,MassifquantParam-method |
| Peak detection in the chromatographic time domain | baseValue baseValue,MatchedFilterParam-method baseValue<- baseValue<-,MatchedFilterParam-method binSize binSize,MatchedFilterParam-method binSize<- binSize<-,MatchedFilterParam-method distance distance,MatchedFilterParam-method distance<- distance<-,MatchedFilterParam-method findChromPeaks,OnDiskMSnExp,MatchedFilterParam-method findChromPeaks-matchedFilter fwhm fwhm,MatchedFilterParam-method fwhm<- fwhm<-,MatchedFilterParam-method impute,MatchedFilterParam-method impute<- impute<-,MatchedFilterParam-method index index,MatchedFilterParam-method index<- index<-,MatchedFilterParam-method matchedFilter MatchedFilterParam MatchedFilterParam-class max,MatchedFilterParam-method max<- max<-,MatchedFilterParam-method mzdiff,MatchedFilterParam-method mzdiff<-,MatchedFilterParam-method sigma sigma,MatchedFilterParam-method sigma<- sigma<-,MatchedFilterParam-method snthresh,MatchedFilterParam-method snthresh<-,MatchedFilterParam-method steps steps,MatchedFilterParam-method steps<- steps<-,MatchedFilterParam-method |
| centWave-based peak detection in purely chromatographic data | findChromPeaks,Chromatogram,CentWaveParam-method findChromPeaks,MChromatograms,CentWaveParam-method findChromPeaks,MChromatograms,MatchedFilterParam-method findChromPeaks-Chromatogram-CentWaveParam |
| matchedFilter-based peak detection in purely chromatographic data | findChromPeaks,Chromatogram,MatchedFilterParam-method |
| Data independent acquisition (DIA): peak detection in isolation windows | findChromPeaksIsolationWindow findChromPeaksIsolationWindow,MsExperiment-method findChromPeaksIsolationWindow,OnDiskMSnExp-method |
| Find fragment ions in xcmsFragment objects | findMZ findMZ,xcmsFragments-method |
| Find neutral losses in xcmsFragment objects | findneutral findneutral,xcmsFragments-method |
| Feature detection for GC/MS and LC/MS Data - methods | findPeaks findPeaks,xcmsRaw-method findPeaks-methods |
| Single-spectrum non-chromatography MS data peak detection | addParams addParams,MSWParam-method addParams<- addParams<-,MSWParam-method ampTh ampTh,MSWParam-method ampTh<- ampTh<-,MSWParam-method findChromPeaks,OnDiskMSnExp,MSWParam-method findPeaks-MSW minNoiseLevel minNoiseLevel,MSWParam-method minNoiseLevel<- minNoiseLevel<-,MSWParam-method MSW MSWParam MSWParam-class nearbyPeak nearbyPeak,MSWParam-method nearbyPeak<- nearbyPeak<-,MSWParam-method peakScaleRange peakScaleRange,MSWParam-method peakScaleRange<- peakScaleRange<-,MSWParam-method peakThr peakThr,MSWParam-method peakThr<- peakThr<-,MSWParam-method ridgeLength ridgeLength,MSWParam-method ridgeLength<- ridgeLength<-,MSWParam-method scales scales,MSWParam-method scales<- scales<-,MSWParam-method snthresh,MSWParam-method snthresh<-,MSWParam-method tuneIn tuneIn,MSWParam-method tuneIn<- tuneIn<-,MSWParam-method verboseColumns,MSWParam-method verboseColumns<-,MSWParam-method |
| Feature detection based on predicted isotope features for high resolution LC/MS data | findPeaks.addPredictedIsotopeFeatures findPeaks.addPredictedIsotopeFeatures,xcmsRaw-method |
| Feature detection for high resolution LC/MS data | findPeaks.centWave findPeaks.centWave,xcmsRaw-method |
| Feature detection with centWave and additional isotope features | findPeaks.centWaveWithPredictedIsotopeROIs findPeaks.centWaveWithPredictedIsotopeROIs,xcmsRaw-method |
| Feature detection for XC-MS data. | findPeaks.massifquant findPeaks.massifquant,xcmsRaw-method |
| Peak detection in the chromatographic time domain | findPeaks.matchedFilter findPeaks.matchedFilter,xcmsRaw-method |
| Collecting MS1 precursor peaks | findPeaks.MS1 findPeaks.MS1,xcmsRaw-method |
| Peak detection for single-spectrum non-chromatography MS data | findPeaks.MSW findPeaks.MSW,xcmsRaw-method |
| Generic parameter class | class:Param GenericParam GenericParam-class Param Param-class |
| Get extracted ion chromatograms for specified m/z ranges | getEIC getEIC,xcmsRaw-method getEIC,xcmsSet-method |
| Get peak intensities for specified regions | getPeaks getPeaks,xcmsRaw-method |
| Get m/z and intensity values for a single mass scan | getMsnScan getMsnScan,xcmsRaw-method getScan getScan,xcmsRaw-method |
| Get average m/z and intensity values for multiple mass scans | getSpec getSpec,xcmsRaw-method |
| Load the raw data for one or more files in the xcmsSet | getXcmsRaw getXcmsRaw,xcmsSet-method |
| Group peaks from different samples together | group group,xcmsSet-method group-methods |
| Group peaks from different samples together | group.density group.density,xcmsSet-method |
| Group Peaks via High Resolution Alignment | group.mzClust group.mzClust,xcmsSet-method |
| Group peaks from different samples together | group.nearest group.nearest,xcmsSet-method |
| Correspondence: group chromatographic peaks across samples | absMz absMz,MzClustParam-method absMz,NearestPeaksParam-method absMz<- absMz<-,MzClustParam-method absMz<-,NearestPeaksParam-method absRt absRt,NearestPeaksParam-method absRt<- absRt<-,NearestPeaksParam-method as.list,PeakDensityParam-method binSize,PeakDensityParam-method binSize<-,PeakDensityParam-method bw bw,PeakDensityParam-method bw<- bw<-,PeakDensityParam-method groupChromPeaks groupChromPeaks,XcmsExperiment,Param-method groupChromPeaks,XCMSnExp,MzClustParam-method groupChromPeaks,XCMSnExp,NearestPeaksParam-method groupChromPeaks,XCMSnExp,PeakDensityParam-method kNN kNN,NearestPeaksParam-method kNN<- kNN<-,NearestPeaksParam-method maxFeatures maxFeatures,PeakDensityParam-method maxFeatures<- maxFeatures<-,PeakDensityParam-method minFraction minFraction,MzClustParam-method minFraction,PeakDensityParam-method minFraction<- minFraction<-,MzClustParam-method minFraction<-,PeakDensityParam-method minSamples minSamples,MzClustParam-method minSamples,PeakDensityParam-method minSamples<- minSamples<-,MzClustParam-method minSamples<-,PeakDensityParam-method MzClustParam MzClustParam-class mzVsRtBalance mzVsRtBalance,NearestPeaksParam-method mzVsRtBalance<- mzVsRtBalance<-,NearestPeaksParam-method NearestPeaksParam NearestPeaksParam-class PeakDensityParam PeakDensityParam-class ppm,MzClustParam-method ppm,PeakDensityParam-method ppm<-,MzClustParam-method sampleGroups sampleGroups,MzClustParam-method sampleGroups,NearestPeaksParam-method sampleGroups,PeakDensityParam-method sampleGroups<- sampleGroups<-,MzClustParam-method sampleGroups<-,NearestPeaksParam-method sampleGroups<-,PeakDensityParam-method |
| Compounding/feature grouping based on similarity of abundances across samples | groupFeatures,XcmsResult,AbundanceSimilarityParam-method groupFeatures-abundance-correlation |
| Compounding/feature grouping based on similarity of extracted ion chromatograms | EicSimilarityParam EicSimilarityParam-class groupFeatures,XcmsResult,EicSimilarityParam-method groupFeatures-eic-similarity |
| Compounding/feature grouping based on similar retention times | groupFeatures,XcmsResult,SimilarRtimeParam-method groupFeatures-similar-rtime |
| Generate unque names for peak groups | groupnames groupnames,xcmsEIC-method groupnames,xcmsSet-method |
| Generate unique group (feature) names based on mass and retention time | groupnames,XCMSnExp-method |
| Group overlapping ranges | groupOverlaps |
| Extract a matrix of peak values for each group | groupval groupval,xcmsSet-method |
| Add definition of chromatographic peaks to an extracted chromatogram plot | highlightChromPeaks |
| Plot log intensity image of a xcmsRaw object | image,xcmsRaw-method |
| Impute values for empty elements in a vector using linear interpolation | imputeLinInterpol |
| Replace missing values with a proportion of the row minimum | imputeRowMin |
| Impute missing values with random numbers based on the row minimum | imputeRowMinRand |
| Extract isolation window target m/z definition | isolationWindowTargetMz isolationWindowTargetMz,OnDiskMSnExp-method |
| Plot log intensity image of a xcmsRaw object | levelplot,xcmsRaw-method levelplot,xcmsSet-method |
| Read binary data from a source | loadRaw loadRaw,xcmsFileSource-method loadRaw,xcmsSource-method loadRaw-methods |
| LC-MS preprocessing result test data sets | faahko_sub faahko_sub2 loadXcmsData xdata xmse |
| Manual peak integration and feature definition | manualChromPeaks manualChromPeaks,MsExperiment-method manualChromPeaks,OnDiskMSnExp-method manualChromPeaks,XcmsExperiment-method manualChromPeaks,XCMSnExp-method manualFeatures manualFeatures,XcmsExperiment-method manualFeatures,XCMSnExp-method |
| Apply a median filter to a matrix | medianFilter |
| Copy MSn data in an xcmsRaw to the MS slots | msn2xcmsRaw |
| Identify overlapping features | overlappingFeatures |
| Plot a grid of a large number of peaks | peakPlots,xcmsSet-method peakPlots-methods |
| Identify peaks in chromatographic data using centWave | peaksWithCentWave |
| Identify peaks in chromatographic data using matchedFilter | peaksWithMatchedFilter |
| Create report of aligned peak intensities | peakTable peakTable,xcmsSet-method |
| Filter features based on the percentage of missing data | filterFeatures,SummarizedExperiment,PercentMissingFilter-method filterFeatures,XcmsResult,PercentMissingFilter-method PercentMissingFilter |
| Derive experimental design from file paths | phenoDataFromPaths |
| Plot extracted ion chromatograms from multiple files | plot, plot-methods plot.xcmsEIC |
| Visualization of Alignment Results | plotAdjustedRtime |
| Plot extracted ion chromatograms from the profile matrix | plotChrom plotChrom,xcmsRaw-method |
| Plot multiple chromatograms into the same plot | plotChromatogramsOverlay plotChromatogramsOverlay,MChromatograms-method plotChromatogramsOverlay,XChromatograms-method |
| Plot chromatographic peak density along the retention time axis | plotChromPeakDensity plotChromPeakDensity,XCMSnExp-method |
| General visualizations of peak detection results | plotChromPeakImage plotChromPeaks |
| Plot extracted ion chromatograms for specified m/z range | plotEIC plotEIC,xcmsRaw-method |
| Plot feature groups in the m/z-retention time space | plotFeatureGroups |
| DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D plot for one sample | plotMsData |
| Plot a grid of a large number of peaks | plotPeaks plotPeaks,xcmsRaw-method |
| General visualization of precursor ions of LC-MS/MS data | plotPrecursorIons |
| Plot m/z and RT deviations for QC purposes without external reference data | plotQC |
| Scatterplot of raw data points | plotRaw plotRaw,xcmsRaw-method |
| Plot retention time deviation profiles | plotrt plotrt,xcmsSet-method |
| Plot a single mass scan | plotScan plotScan,xcmsRaw-method |
| Plot mass spectra from the profile matrix | plotSpec plotSpec,xcmsRaw-method |
| Plot profile matrix 3D surface using OpenGL | plotSurf plotSurf,xcmsRaw-method |
| Plot total ion count | plotTIC plotTIC,xcmsRaw-method |
| Tracking data processing | fileIndex fileIndex,ProcessHistory-method msLevel,XProcessHistory-method processDate processDate,ProcessHistory-method ProcessHistory ProcessHistory-class processInfo processInfo,ProcessHistory-method processParam processParam,XProcessHistory-method processType processType,ProcessHistory-method show,ProcessHistory-method show,XProcessHistory-method XProcessHistory XProcessHistory-class |
| The profile matrix | profile-matrix profMat profMat,MsExperiment-method profMat,xcmsRaw-method profMat-xcmsSet |
| Median filtering of the profile matrix | profMedFilt profMedFilt,xcmsRaw-method |
| Get and set method for generating profile data | profMethod profMethod,xcmsRaw-method profMethod<- profMethod<-,xcmsRaw-method |
| Specify a subset of profile mode data | profRange profRange,xcmsRaw-method |
| Get and set m/z step for generating profile data | profStep profStep,xcmsRaw-method profStep<- profStep<-,xcmsRaw-method |
| Accessing mz-rt feature data values | featureValues featureValues,XCMSnExp-method quantify,XCMSnExp-method |
| Get extracted ion chromatograms for specified m/z range | rawEIC rawEIC,xcmsRaw-method |
| Get a raw data matrix | rawMat rawMat,xcmsRaw-method rawMat-methods |
| Data independent acquisition (DIA): reconstruct MS2 spectra | reconstructChromPeakSpectra reconstructChromPeakSpectra,XcmsExperiment-method reconstructChromPeakSpectra,XCMSnExp-method |
| Refine Identified Chromatographic Peaks | CleanPeaksParam CleanPeaksParam-class FilterIntensityParam FilterIntensityParam-class MergeNeighboringPeaksParam MergeNeighboringPeaksParam-class refineChromPeaks refineChromPeaks,XcmsExperiment,CleanPeaksParam-method refineChromPeaks,XcmsExperiment,FilterIntensityParam-method refineChromPeaks,XcmsExperiment,MergeNeighboringPeaksParam-method refineChromPeaks,XCMSnExp,CleanPeaksParam-method refineChromPeaks,XCMSnExp,FilterIntensityParam-method refineChromPeaks,XCMSnExp,MergeNeighboringPeaksParam-method show,CleanPeaksParam-method show,FilterIntensityParam-method show,MergeNeighboringPeaksParam-method |
| Remove intensities from chromatographic data | removeIntensity removeIntensity,Chromatogram-method removeIntensity,MChromatograms-method removeIntensity,XChromatogram-method |
| Correct retention time from different samples | retcor retcor,xcmsSet-method retcor-methods |
| Align retention times across samples with Obiwarp | retcor.obiwarp retcor.obiwarp,xcmsSet-method |
| Align retention times across samples | retcor.linear retcor.linear,xcmsSet-method retcor.loess retcor.loess,xcmsSet-method retcor.peakgroups retcor.peakgroups,xcmsSet-method |
| Set retention time window to a specified width | retexp |
| Calculate relative log abundances | rla rowRla |
| Filter features based on their coefficient of variation | filterFeatures,SummarizedExperiment,RsdFilter-method filterFeatures,XcmsResult,RsdFilter-method RsdFilter |
| Get sample names | sampnames sampnames,xcmsEIC-method sampnames,xcmsSet-method |
| Extract processing errors | showError showError,xcmsSet-method |
| Distance methods for xcmsSet, xcmsRaw and xsAnnotate | specDist specDist,xcmsSet-method specDist-methods |
| a Distance function based on matching peaks | specDist.cosine specDist.cosine,matrix,matrix-method |
| a Distance function based on matching peaks | specDist.meanMZmatch specDist.meanMZmatch,matrix,matrix-method |
| a Distance function based on matching peaks | specDist.peakCount specDist.peakCount,matrix,matrix-method specDist.peakCount-methods |
| Calculate noise for a sparse continuum mass spectrum | specNoise |
| Identify peaks in a sparse continuum mode spectrum | specPeaks |
| Divide an xcmsRaw object | split.xcmsRaw |
| Divide an xcmsSet object | split, split-methods split.xcmsSet |
| Gaussian Model | SSgauss |
| Correct gaps in data | makeacqNum makeacqNum, xcmsRaw-method stitch stitch,xcmsRaw-method stitch-methods stitch.netCDF stitch.xml |
| Update an 'xcmsSet' object | updateObject,xcmsSet-method |
| Enable usage of old xcms code | useOriginalCode |
| Verify an mzQuantML file | verify.mzQuantML |
| Save an xcmsRaw object to file | write.cdf write.cdf,xcmsRaw-method |
| Save an xcmsRaw object to a file | write.mzdata write.mzdata,xcmsRaw-method |
| Save an xcmsSet object to an PSI mzQuantML file | write.mzQuantML write.mzQuantML,xcmsSet-method |
| Export MS data to mzML/mzXML files | writeMSData,XCMSnExp,character-method |
| Save a grouped xcmsSet object in mzTab-1.1 format file | writeMzTab |
| Containers for chromatographic and peak detection data | chromPeakData,XChromatogram-method chromPeakData,XChromatograms-method chromPeakData<-,XChromatogram-method chromPeaks,XChromatogram-method chromPeaks,XChromatograms-method chromPeaks<-,XChromatogram-method coerce,MChromatograms,XChromatograms-method dropFeatureDefinitions,XChromatograms-method dropFilledChromPeaks,XChromatogram-method dropFilledChromPeaks,XChromatograms-method featureDefinitions,XChromatograms-method featureValues,XChromatograms-method filterChromPeaks,XChromatogram-method filterChromPeaks,XChromatograms-method filterMz,XChromatogram-method filterMz,XChromatograms-method filterRt,XChromatogram-method filterRt,XChromatograms-method groupChromPeaks,XChromatograms,PeakDensityParam-method hasChromPeaks,XChromatogram-method hasChromPeaks,XChromatograms-method hasFeatures,XChromatograms-method hasFilledChromPeaks,XChromatograms-method plot,XChromatogram,ANY-method plot,XChromatograms,ANY-method plotChromPeakDensity,XChromatograms-method processHistory,XChromatograms-method refineChromPeaks,XChromatogram,MergeNeighboringPeaksParam-method refineChromPeaks,XChromatograms,MergeNeighboringPeaksParam-method show,XChromatogram-method show,XChromatograms-method transformIntensity,XChromatogram-method transformIntensity,XChromatograms-method XChromatogram XChromatogram-class XChromatograms XChromatograms-class [,XChromatograms,ANY,ANY,ANY-method |
| Deprecated functions in package 'xcms' | xcms-deprecated |
| Class xcmsEIC, a class for multi-sample extracted ion chromatograms | mzrange mzrange,xcmsEIC-method rtrange rtrange,xcmsEIC-method show,xcmsEIC-method xcmsEIC-class |
| Base class for loading raw data from a file | xcmsFileSource-class xcmsSource,character-method |
| Constructor for xcmsFragments objects which holds Tandem MS peaks | xcmsFragments |
| Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data | plotTree plotTree,xcmsFragments-method show,xcmsFragments-method xcmsFragments-class |
| Data container storing xcms preprocessing results | adjustedRtime adjustedRtime,MsFeatureData-method adjustedRtime,XCMSnExp-method adjustedRtime<- adjustedRtime<-,MsFeatureData-method adjustedRtime<-,XCMSnExp-method c.XCMSnExp chromPeakData chromPeakData,MsFeatureData-method chromPeakData,XCMSnExp-method chromPeakData<- chromPeakData<-,MsFeatureData-method chromPeakData<-,XCMSnExp-method chromPeaks chromPeaks,MsFeatureData-method chromPeaks,XCMSnExp-method chromPeaks<- chromPeaks<-,MsFeatureData-method chromPeaks<-,XCMSnExp-method dropAdjustedRtime dropAdjustedRtime,MsFeatureData-method dropAdjustedRtime,XCMSnExp-method dropChromPeaks dropChromPeaks,MsFeatureData-method dropChromPeaks,XCMSnExp-method dropFeatureDefinitions dropFeatureDefinitions,MsFeatureData-method dropFeatureDefinitions,XCMSnExp-method dropFilledChromPeaks dropFilledChromPeaks,XCMSnExp-method featureDefinitions featureDefinitions,MsFeatureData-method featureDefinitions,XCMSnExp-method featureDefinitions<- featureDefinitions<-,MsFeatureData-method featureDefinitions<-,XCMSnExp-method findChromPeaks,XCMSnExp,Param-method hasAdjustedRtime hasAdjustedRtime,MsFeatureData-method hasAdjustedRtime,OnDiskMSnExp-method hasAdjustedRtime,XCMSnExp-method hasChromPeaks hasChromPeaks,MsFeatureData-method hasChromPeaks,XCMSnExp-method hasFeatures hasFeatures,MsFeatureData-method hasFeatures,XCMSnExp-method hasFilledChromPeaks hasFilledChromPeaks,XCMSnExp-method intensity,XCMSnExp-method mz,XCMSnExp-method plot,XCMSnExp,missing-method processHistory processHistory,XCMSnExp-method processHistoryTypes profMat,OnDiskMSnExp-method profMat,XCMSnExp-method rtime,XCMSnExp-method setAs show,MsFeatureData-method show,XCMSnExp-method spectra,XCMSnExp-method spectrapply,XCMSnExp-method updateObject,XCMSnExp-method XCMSnExp XCMSnExp-class |
| A matrix of peaks | show,xcmsPeaks-method xcmsPeaks-class |
| Constructor for xcmsRaw objects which reads NetCDF/mzXML files | deepCopy deepCopy,xcmsRaw-method xcmsRaw |
| Class xcmsRaw, a class for handling raw data | findmzROI findmzROI,xcmsRaw-method levelplot mslevel,xcmsRaw-method profinfo,xcmsRaw-method profMz profMz,xcmsRaw-method revMz revMz,xcmsRaw-method scanrange,xcmsRaw-method show,xcmsRaw-method sortMz sortMz,xcmsRaw-method xcmsRaw-class |
| Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files | xcmsSet |
| Class xcmsSet, a class for preprocessing peak data | $,xcmsSet-method $<-,xcmsSet-method filepaths filepaths,xcmsSet-method filepaths<- filepaths<-,xcmsSet-method groupidx groupidx,xcmsSet-method groupidx<- groupidx<-,xcmsSet-method groups groups,xcmsSet-method groups<- groups<-,xcmsSet-method mslevel mslevel,xcmsSet-method peaks peaks,xcmsSet-method peaks<- peaks<-,xcmsSet-method phenoData phenoData,xcmsSet-method phenoData<- phenoData<-,xcmsSet,ANY-method phenoData<-,xcmsSet-method profinfo profinfo,xcmsSet-method profinfo<- profinfo<-,xcmsSet-method profMethod,xcmsSet-method profStep,xcmsSet-method progressCallback progressCallback,xcmsSet-method progressCallback<- progressCallback<-,xcmsSet-method sampclass sampclass,xcmsSet-method sampclass<- sampclass<-,xcmsSet-method sampnames<- sampnames<-,xcmsSet-method scanrange scanrange,xcmsSet-method show,xcmsSet-method xcmsSet-class [,xcmsSet,ANY,ANY,ANY-method [,xcmsSet-method |
| Virtual class for raw data sources | xcmsSource-class |
| Create an 'xcmsSource' object in a flexible way | xcmsSource xcmsSource,xcmsSource-method xcmsSource-methods |
