├── .BBSoptions ├── .Rbuildignore ├── .editorconfig ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── AllGenerics.R ├── DataClasses.R ├── Deprecated.R ├── MPI.R ├── MsExperiment-functions.R ├── MsExperiment.R ├── XcmsExperiment-functions.R ├── XcmsExperiment-plotting.R ├── XcmsExperiment.R ├── XcmsExperimentHdf5-functions.R ├── XcmsExperimentHdf5.R ├── c.R ├── cwTools.R ├── databases.R ├── do_adjustRtime-functions.R ├── do_findChromPeaks-functions.R ├── do_groupChromPeaks-functions.R ├── fastMatch.R ├── functions-Chromatogram.R ├── functions-IO.R ├── functions-MsFeatureData.R ├── functions-OnDiskMSnExp.R ├── functions-Params.R ├── functions-ProcessHistory.R ├── functions-XCMSnExp.R ├── functions-XChromatogram.R ├── functions-XChromatograms.R ├── functions-binning.R ├── functions-imputation.R ├── functions-utils.R ├── functions-xcmsEIC.R ├── functions-xcmsFragments.R ├── functions-xcmsRaw.R ├── functions-xcmsSet.R ├── functions-xcmsSwath.R ├── hidden_aliases.R ├── init.R ├── loadXcmsData.R ├── matchpeaks.R ├── method-filterFeatures.R ├── methods-Chromatogram.R ├── methods-IO.R ├── methods-MChromatograms.R ├── methods-MsFeatureData.R ├── methods-OnDiskMSnExp.R ├── methods-Params.R ├── methods-ProcessHistory.R ├── methods-XCMSnExp.R ├── methods-XChromatogram.R ├── methods-XChromatograms.R ├── methods-group-features.R ├── methods-xcmsEIC.R ├── methods-xcmsFileSource.R ├── methods-xcmsFragments.R ├── methods-xcmsPeaks.R ├── methods-xcmsRaw.R ├── methods-xcmsSet.R ├── models.R ├── mzClust.R ├── plotQC.R ├── specDist.R ├── write.mzquantML.R ├── writemzdata.R ├── writemztab.R ├── xcmsSource.R └── zzz.R ├── README.md ├── _pkgdown.yml ├── data ├── faahko_sub.RData ├── faahko_sub2.RData ├── xdata.RData └── xmse.RData ├── inst ├── CHANGELOG ├── CITATION ├── mgf │ ├── metlin-2724.mgf │ ├── metlin-68898.mgf │ └── metlin-72445.mgf └── xsd │ └── mzQuantML_1_0_0.xsd ├── logo.png ├── longtests ├── testthat.R └── testthat │ ├── test_do_adjustRtime-functions.R │ ├── test_do_findChromPeaks-functions.R │ ├── test_do_groupChromPeaks-functions.R │ ├── test_functions-OnDiskMSnExp.R │ ├── test_methods-OnDiskMSnExp.R │ ├── test_methods-XCMSnExp.R │ ├── test_old_BiocParallel.R │ ├── test_old_absentPresent.R │ ├── test_old_functions-IO.R │ ├── test_old_functions-xcmsRaw.R │ ├── test_old_functions-xcmsSet.R │ ├── test_old_methods-IO.R │ ├── test_old_methods-xcmsRaw.R │ ├── test_old_methods-xcmsSet.R │ ├── test_old_xcmsSource.R │ └── test_specDist.R ├── man ├── AutoLockMass-methods.Rd ├── BlankFlag.Rd ├── DratioFilter.Rd ├── GenericParam.Rd ├── LamaParama.Rd ├── PercentMissingFilter.Rd ├── ProcessHistory-class.Rd ├── RsdFilter.Rd ├── SSgauss.Rd ├── XCMSnExp-class.Rd ├── XCMSnExp-filter-methods.Rd ├── XCMSnExp-inherited-methods.Rd ├── XCMSnExp-peak-grouping-results.Rd ├── XChromatogram.Rd ├── XcmsExperiment.Rd ├── XcmsExperimentHdf5.Rd ├── absent-methods.Rd ├── adjustRtime.Rd ├── applyAdjustedRtime.Rd ├── binYonX.Rd ├── breaks_on_binSize.Rd ├── breaks_on_nBins.Rd ├── c.xcmsSet.Rd ├── calibrate-calibrant-mass.Rd ├── calibrate.Rd ├── chromPeakChromatograms.Rd ├── chromPeakSpectra.Rd ├── chromPeakSummary.Rd ├── chromatogram-method.Rd ├── colMax.Rd ├── collect-methods.Rd ├── correlate-Chromatogram.Rd ├── descendZero.Rd ├── diffreport-methods.Rd ├── dirname.Rd ├── do_adjustRtime_peakGroups.Rd ├── do_findChromPeaks_centWave.Rd ├── do_findChromPeaks_centWaveWithPredIsoROIs.Rd ├── do_findChromPeaks_massifquant.Rd ├── do_findChromPeaks_matchedFilter.Rd ├── do_findPeaks_MSW.Rd ├── do_groupChromPeaks_density.Rd ├── do_groupChromPeaks_nearest.Rd ├── do_groupPeaks_mzClust.Rd ├── doubleMatrix.Rd ├── estimatePrecursorIntensity.Rd ├── etg.Rd ├── exportMetaboAnalyst.Rd ├── extractMsData-method.Rd ├── feature-grouping.Rd ├── featureChromatograms.Rd ├── featureSpectra.Rd ├── featureSummary.Rd ├── figures │ └── logo.png ├── fillChromPeaks.Rd ├── fillPeaks-methods.Rd ├── fillPeaks.MSW-methods.Rd ├── fillPeaks.chrom-methods.Rd ├── filter-MChromatograms.Rd ├── filterFeatures.Rd ├── filtfft.Rd ├── findChromPeaks-Chromatogram-CentWaveParam.Rd ├── findChromPeaks-Chromatogram-MatchedFilter.Rd ├── findChromPeaks-centWave.Rd ├── findChromPeaks-centWaveWithPredIsoROIs.Rd ├── findChromPeaks-massifquant.Rd ├── findChromPeaks-matchedFilter.Rd ├── findChromPeaks.Rd ├── findChromPeaksIsolationWindow.Rd ├── findEqualGreater.Rd ├── findMZ.Rd ├── findPeaks-MSW.Rd ├── findPeaks-methods.Rd ├── findPeaks.MS1-methods.Rd ├── findPeaks.MSW-xcmsRaw-method.Rd ├── findPeaks.addPredictedIsotopeFeatures-methods.Rd ├── findPeaks.centWave-methods.Rd ├── findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd ├── findPeaks.massifquant-methods.Rd ├── findPeaks.matchedFilter-xcmsRaw-method.Rd ├── findneutral.Rd ├── getEIC-methods.Rd ├── getPeaks-methods.Rd ├── getScan-methods.Rd ├── getSpec-methods.Rd ├── getXcmsRaw-methods.Rd ├── group-methods.Rd ├── group.density.Rd ├── group.mzClust.Rd ├── group.nearest.Rd ├── groupChromPeaks.Rd ├── groupFeatures-abundance-correlation.Rd ├── groupFeatures-eic-similarity.Rd ├── groupFeatures-similar-rtime.Rd ├── groupOverlaps.Rd ├── groupnames-XCMSnExp.Rd ├── groupnames-methods.Rd ├── groupval-methods.Rd ├── hidden_aliases.Rd ├── highlightChromPeaks.Rd ├── image.xcmsRaw.Rd ├── imputeLinInterpol.Rd ├── imputeRowMin.Rd ├── imputeRowMinRand.Rd ├── isolationWindowTargetMz-OnDiskMSnExp-method.Rd ├── levelplot.xcmsRaw.Rd ├── loadRaw-methods.Rd ├── loadXcmsData.Rd ├── manualChromPeaks.Rd ├── medianFilter.Rd ├── msn2xcmsRaw.Rd ├── na.flatfill.Rd ├── overlappingFeatures.Rd ├── panel.cor.Rd ├── peakPlots-methods.Rd ├── peakTable-methods.Rd ├── peaksWithCentWave.Rd ├── peaksWithMatchedFilter.Rd ├── phenoDataFromPaths.Rd ├── plot.xcmsEIC.Rd ├── plotAdjustedRtime.Rd ├── plotChrom-methods.Rd ├── plotChromPeakDensity.Rd ├── plotChromPeaks.Rd ├── plotChromatogramsOverlay.Rd ├── plotEIC-methods.Rd ├── plotFeatureGroups.Rd ├── plotMsData.Rd ├── plotPeaks-methods.Rd ├── plotPrecursorIons.Rd ├── plotQC.Rd ├── plotRaw-methods.Rd ├── plotScan-methods.Rd ├── plotSpec-methods.Rd ├── plotSurf-methods.Rd ├── plotTIC-methods.Rd ├── plotrt-methods.Rd ├── profGenerate.Rd ├── profMat-xcmsSet.Rd ├── profMedFilt-methods.Rd ├── profMethod-methods.Rd ├── profRange-methods.Rd ├── profStep-methods.Rd ├── pval.Rd ├── rawEIC-methods.Rd ├── rawMat-methods.Rd ├── reconstructChromPeakSpectra.Rd ├── rectUnique.Rd ├── refineChromPeaks.Rd ├── removeIntensity-Chromatogram.Rd ├── retcor-methods.Rd ├── retcor.obiwarp-methods.Rd ├── retcor.peakgroups-methods.Rd ├── retexp.Rd ├── rla.Rd ├── sampnames-methods.Rd ├── showError-xcmsSet-method.Rd ├── specDist-methods.Rd ├── specDist.cosine-methods.Rd ├── specDist.meanMZmatch-methods.Rd ├── specDist.peakCount-methods.Rd ├── specNoise.Rd ├── specPeaks.Rd ├── split.xcmsRaw.Rd ├── split.xcmsSet.Rd ├── stitch-methods.Rd ├── sub-xcmsRaw-logicalOrNumeric-missing-missing-method.Rd ├── updateObject-xcmsSet-method.Rd ├── useOriginalCode.Rd ├── verify.mzQuantML.Rd ├── write.cdf-methods.Rd ├── write.mzQuantML.Rd ├── write.mzdata-methods.Rd ├── writeMSData-XCMSnExp-character-method.Rd ├── writeMzTab.Rd ├── xcms-deprecated.Rd ├── xcmsEIC-class.Rd ├── xcmsFileSource-class.Rd ├── xcmsFragments-class.Rd ├── xcmsFragments.Rd ├── xcmsPeaks-class.Rd ├── xcmsRaw-class.Rd ├── xcmsRaw.Rd ├── xcmsSet-class.Rd ├── xcmsSet.Rd ├── xcmsSource-class.Rd └── xcmsSource-methods.Rd ├── src ├── Makevars ├── Makevars.win ├── binarySearch.h ├── binners.c ├── binners.h ├── fastMatch.c ├── massifquant │ ├── DataKeeper.cpp │ ├── DataKeeper.h │ ├── OpOverload.cpp │ ├── OpOverload.h │ ├── SegProc.cpp │ ├── SegProc.h │ ├── TrMgr.cpp │ ├── TrMgr.h │ ├── Tracker.cpp │ ├── Tracker.h │ ├── dpq.h │ ├── nmath.h │ └── xcms_massifquant.cpp ├── mzClust_hclust.c ├── mzROI.c ├── obiwarp │ ├── lmat.h │ ├── mat.cpp │ ├── mat.h │ ├── vec.cpp │ ├── vec.h │ ├── xcms_dynprog.cpp │ ├── xcms_dynprog.h │ └── xcms_lmat.cpp ├── util.c ├── util.h ├── xcms.c ├── xcms.h └── xcms_obiwarp.cpp ├── tests ├── testthat.R └── testthat │ ├── test_Chromatogram.R │ ├── test_MsExperiment-functions.R │ ├── test_MsExperiment.R │ ├── test_MsFeatureData.R │ ├── test_Param_classes.R │ ├── test_XcmsExperiment-functions.R │ ├── test_XcmsExperiment-plotting.R │ ├── test_XcmsExperiment.R │ ├── test_XcmsExperimentHdf5-functions.R │ ├── test_XcmsExperimentHdf5.R │ ├── test_do_adjustRtime-functions.R │ ├── test_do_findChromPeaks-functions.R │ ├── test_do_groupChromPeaks-functions.R │ ├── test_function-filtering.R │ ├── test_functions-Chromatogram.R │ ├── test_functions-OnDiskMSnExp.R │ ├── test_functions-ProcessHistory.R │ ├── test_functions-XCMSnExp.R │ ├── test_functions-XChromatogram.R │ ├── test_functions-XChromatograms.R │ ├── test_functions-binning.R │ ├── test_functions-imputation.R │ ├── test_functions-utils.R │ ├── test_functions-xcmsSwath.R │ ├── test_loadXcmsData.R │ ├── test_matchpeaks.R │ ├── 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