Files in yclement/xcms

LC-MS and GC-MS Data Analysis

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-XChromatogram.R R/functions-XChromatograms.R R/functions-binning.R R/functions-imputation.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/functions-xcmsSwath.R R/init.R R/matchpeaks.R R/methods-Chromatogram.R R/methods-Chromatograms.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-XChromatogram.R R/methods-XChromatograms.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/mzClust.R R/netCDF.R R/plotQC.R R/ramp.R R/remove-MsCoreUtils-function.R R/specDist.R R/write.mzquantML.R R/writemzdata.R R/writemztab.R R/xcmsSource.R R/zzz.R README.md man/AutoLockMass-methods.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/XChromatogram.Rd man/absent-methods.Rd man/adjustRtime-obiwarp.Rd man/adjustRtime-peakGroups.Rd man/adjustRtime.Rd man/align-Chromatogram.Rd man/applyAdjustedRtime.Rd man/binYonX.Rd man/breaks_on_binSize.Rd man/breaks_on_nBins.Rd man/c.xcmsSet.Rd man/calibrate-calibrant-mass.Rd man/calibrate.Rd man/chromPeakSpectra.Rd man/chromatogram-method.Rd man/chromatographic-peak-detection.Rd man/colMax.Rd man/collect-methods.Rd man/correlate-Chromatogram.Rd man/descendZero.Rd man/diffreport-methods.Rd man/dirname.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/exportMetaboAnalyst.Rd man/extractMsData-method.Rd man/featureChromatograms.Rd man/featureSpectra.Rd man/featureSummary.Rd man/fillChromPeaks.Rd man/fillPeaks-methods.Rd man/fillPeaks.MSW-methods.Rd man/fillPeaks.chrom-methods.Rd man/filtfft.Rd man/findChromPeaks-Chromatogram-CentWaveParam.Rd man/findChromPeaks-Chromatogram-MatchedFilter.Rd man/findChromPeaks-centWave.Rd man/findChromPeaks-centWaveWithPredIsoROIs.Rd man/findChromPeaks-massifquant.Rd man/findChromPeaks-matchedFilter.Rd man/findChromPeaksIsolationWindow.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/groupOverlaps.Rd man/groupnames-XCMSnExp.Rd man/groupnames-methods.Rd man/groupval-methods.Rd man/highlightChromPeaks.Rd man/image.xcmsRaw.Rd man/imputeLinInterpol.Rd man/imputeRowMin.Rd man/imputeRowMinRand.Rd man/isolationWindowTargetMz-OnDiskMSnExp-method.Rd man/levelplot.xcmsRaw.Rd man/loadRaw-methods.Rd man/medianFilter.Rd man/msn2xcmsRaw.Rd man/na.flatfill.Rd man/overlappingFeatures.Rd man/panel.cor.Rd man/peakPlots-methods.Rd man/peakTable-methods.Rd man/peaksWithCentWave.Rd man/peaksWithMatchedFilter.Rd man/phenoDataFromPaths.Rd man/plot.xcmsEIC.Rd man/plotAdjustedRtime.Rd man/plotChrom-methods.Rd man/plotChromPeakDensity.Rd man/plotChromPeaks.Rd man/plotEIC-methods.Rd man/plotMsData.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/reconstructChromPeakSpectra.Rd man/rectUnique.Rd man/refineChromPeaks-clean.Rd man/refineChromPeaks-merge.Rd man/retcor-methods.Rd man/retcor.obiwarp-methods.Rd man/retcor.peakgroups-methods.Rd man/retexp.Rd man/rla.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/writeMSData-XCMSnExp-character-method.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 tests/testthat.R tests/testthat/test_Chromatogram.R tests/testthat/test_MsFeatureData.R tests/testthat/test_Param_classes.R tests/testthat/test_do_adjustRtime-functions.R tests/testthat/test_do_findChromPeaks-functions.R tests/testthat/test_do_groupChromPeaks-functions.R tests/testthat/test_functions-Chromatogram.R tests/testthat/test_functions-OnDiskMSnExp.R tests/testthat/test_functions-ProcessHistory.R tests/testthat/test_functions-XCMSnExp.R tests/testthat/test_functions-XChromatogram.R tests/testthat/test_functions-XChromatograms.R tests/testthat/test_functions-binning.R tests/testthat/test_functions-imputation.R tests/testthat/test_functions-normalization.R tests/testthat/test_functions-utils.R tests/testthat/test_functions-xcmsSwath.R tests/testthat/test_matchpeaks.R tests/testthat/test_methods-Chromatogram.R tests/testthat/test_methods-Chromatograms.R tests/testthat/test_methods-OnDiskMSnExp.R tests/testthat/test_methods-XCMSnExp.R tests/testthat/test_methods-XChromatogram.R tests/testthat/test_methods-XChromatograms.R tests/testthat/test_old_BiocParallel.R tests/testthat/test_old_absentPresent.R tests/testthat/test_old_functions-IO.R tests/testthat/test_old_functions-xcmsRaw.R tests/testthat/test_old_functions-xcmsSet.R tests/testthat/test_old_methods-IO.R tests/testthat/test_old_methods-xcmsRaw.R tests/testthat/test_old_methods-xcmsSet.R tests/testthat/test_old_xcmsSource.R tests/testthat/test_specDist.R vignettes/new_functionality.Rmd vignettes/xcms-direct-injection.Rmd vignettes/xcms-lcms-ms.Rmd vignettes/xcms.Rmd