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.

AuthorColin A. Smith <csmith@scripps.edu>, Ralf Tautenhahn <rtautenh@gmail.com>, Steffen Neumann <sneumann@ipb-halle.de>, Paul Benton <hpbenton@scripps.edu>, Christopher Conley <cjconley@ucdavis.edu>, Johannes Rainer <Johannes.Rainer@eurac.edu>
Date of publicationNone
MaintainerSteffen Neumann <sneumann@ipb-halle.de>
LicenseGPL (>= 2) + file LICENSE
Version1.50.1
http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms

View on Bioconductor

Man pages

absent-methods: Determine which peaks are absent / present in a sample class

AutoLockMass-methods: Automatic parameter for Lock mass fixing 'AutoLockMass' ~~

calibrate: Calibrate peaks for correcting unprecise m/z values

collect-methods: Collect MS^n peaks into xcmsFragments

colMax: Find row and column maximum values

c.xcmsSet: Combine xcmsSet objects

descendZero: Find start and end points of a peak

diffreport-methods: Create report of analyte differences

doubleMatrix: Allocate double, integer, or logical matricies

etg: Empirically Transformed Gaussian function

fillPeaks.chrom-methods: Integrate areas of missing peaks

fillPeaks-methods: Integrate areas of missing peaks

fillPeaks.MSW-methods: Integrate areas of missing peaks in FTICR-MS data

filtfft: Apply an convolution filter using an FFT

findEqualGreater: Find values in sorted vectors

findMZ: Find fragment ions in xcmsFragment objects

findneutral: Find neutral losses in xcmsFragment objects

findPeaks.addPredictedIsotopeFeatures-methods: Feature detection based on predicted isotope features for...

findPeaks.centWave-methods: Feature detection for high resolution LC/MS data

findPeaks.centWaveWithPredictedIsotopeROIs-methods: Feature detection with centWave and additional isotope...

findPeaks.massifquant-methods: Feature detection for XC-MS data.

findPeaks.matchedFilter-methods: Feature detection in the chromatographic time domain

findPeaks-methods: Feature detection for GC/MS and LC/MS Data - methods

findPeaks.MS1-methods: Collecting MS1 precursor peaks

findPeaks.MSW-methods: Feature detection for single-spectrum non-chromatography MS...

getEIC-methods: Get extracted ion chromatograms for specified m/z ranges

getPeaks-methods: Get peak intensities for specified regions

getScan-methods: Get m/z and intensity values for a single mass scan

getSpec-methods: Get average m/z and intensity values for multiple mass scans

getXcmsRaw-methods: Load the raw data for one or more files in the xcmsSet

group.density: Group peaks from different samples together

group-methods: Group peaks from different samples together

group.mzClust: Group Peaks via High Resolution Alignment

groupnames-methods: Generate unque names for peak groups

group.nearest: Group peaks from different samples together

groupval-methods: Extract a matrix of peak values for each group

image.xcmsRaw: Plot log intensity image of a xcmsRaw object

levelplot.xcmsRaw: Plot log intensity image of a xcmsRaw object

loadRaw-methods: Read binary data from a source

medianFilter: Apply a median filter to a matrix

msn2xcmsRaw: Copy MSn data in an xcmsRaw to the MS slots

na.flatfill: Fill in NA values at the extremes of a vector

netCDF: High-performance, low-level access to NetCDF data files

netCdfSource-class: Class '"netCdfSource"', for reading raw data from 'netCDF'...

panel.cor: Correlation coefficient panel for pairs function

peakPlots-methods: Plot a grid of a large number of peaks

peakTable-methods: Create report of aligned peak intensities

plotChrom-methods: Plot extracted ion chromatograms from the profile matrix

plotEIC-methods: Plot extracted ion chromatograms for specified m/z range

plotPeaks-methods: Plot a grid of a large number of peaks

plotQC: Plot m/z and RT deviations for QC purposes without external...

plotRaw-methods: Scatterplot of raw data points

plotrt-methods: Plot retention time deviation profiles

plotScan-methods: Plot a single mass scan

plotSpec-methods: Plot mass spectra from the profile matrix

plotSurf-methods: Plot profile matrix 3D surface using OpenGL

plotTIC-methods: Plot total ion count

plot.xcmsEIC: Plot extracted ion chromatograms from multiple files

profGenerate: Generation of profile data

profMedFilt-methods: Median filtering of the profile matrix

profMethod-methods: Get and set method for generating profile data

profRange-methods: Specify a subset of profile mode data

profStep-methods: Get and set m/z step for generating profile data

pval: Generate p-values for a vector of t-statistics

rampSource-class: Class '"rampSource"', for reading raw data from 'netCDF'...

rawEIC-methods: Get extracted ion chromatograms for specified m/z range

rawMat-methods: Get a raw data matrix

rectUnique: Determine a subset of rectangles with unique, non-overlapping...

retcor-methods: Correct retention time from different samples

retcor.obiwarp-methods: Align retention times across samples with Obiwarp

retcor.peakgroups-methods: Align retention times across samples

retexp: Set retention time window to a specified width

sampnames-methods: Get sample names

specDist.cosine-methods: a Distance function based on matching peaks

specDist.meanMZmatch-methods: a Distance function based on matching peaks

specDist-methods: Distance methods for xcmsSet, xcmsRaw and xsAnnotate

specDist.peakCount-methods: a Distance function based on matching peaks

specNoise: Calculate noise for a sparse continuum mass spectrum

specPeaks: Identify peaks in a sparse continuum mode spectrum

split.xcmsRaw: Divide an xcmsRaw object

split.xcmsSet: Divide an xcmsSet object

SSgauss: Gaussian Model

stitch-methods: Correct gaps in data

updateObject-xcmsSet-method: Update an 'xcmsSet' object

valueCount2ScanIndex: Create index vector for internal C calls

verify.mzQuantML: Verify an mzQuantML file

write.cdf-methods: Save an xcmsRaw object to file

write.mzdata-methods: Save an xcmsRaw object to a file

write.mzQuantML: Save an xcmsSet object to an PSI mzQuantML file

writeMzTab: Save a grouped xcmsSet object in mzTab-1.1 format file

xcms-deprecated: Deprecated functions in package 'xcms'

xcmsEIC-class: Class xcmsEIC, a class for multi-sample extracted ion...

xcmsFileSource-class: Base class for loading raw data from a file

xcmsFragments: Constructor for xcmsFragments objects which holds Tandem MS...

xcmsFragments-class: Class xcmsFragments, a class for handling Tandem MS and...

xcmsPapply: _Deprecated_: xcmsPapply

xcmsPeaks-class: A matrix of peaks

xcmsRaw: Constructor for xcmsRaw objects which reads NetCDF/mzXML...

xcmsRaw-class: Class xcmsRaw, a class for handling raw data

xcmsSet: Constructor for xcmsSet objects which finds peaks in...

xcmsSet-class: Class xcmsSet, a class for preprocessing peak data

xcmsSource-class: Virtual class for raw data sources

xcmsSource-methods: Create an 'xcmsSource' object in a flexible way

Files in this package

xcms/DESCRIPTION
xcms/LICENSE
xcms/NAMESPACE
xcms/R
xcms/R/AllGenerics.R xcms/R/DataClasses.R xcms/R/Deprecated.R xcms/R/MPI.R xcms/R/c.R xcms/R/cwTools.R xcms/R/databases.R xcms/R/do_detectFeatures-functions.R xcms/R/fastMatch.R xcms/R/functions-binning.R xcms/R/functions-utils.R xcms/R/functions-xcmsEIC.R xcms/R/functions-xcmsFragments.R xcms/R/functions-xcmsRaw.R xcms/R/functions-xcmsSet.R xcms/R/init.R xcms/R/matchpeaks.R xcms/R/methods-IO.R xcms/R/methods-netCdfSource.R xcms/R/methods-rampSource.R xcms/R/methods-xcmsEIC.R xcms/R/methods-xcmsFragments.R xcms/R/methods-xcmsPeaks.R xcms/R/methods-xcmsRaw.R xcms/R/methods-xcmsSet.R xcms/R/models.R xcms/R/msn2xcmsRaw.R xcms/R/mzClust.R xcms/R/netCDF.R xcms/R/plotQC.R xcms/R/ramp.R xcms/R/specDist.R
xcms/R/unix
xcms/R/windows
xcms/R/write.mzquantML.R xcms/R/writemzdata.R xcms/R/writemztab.R xcms/R/xcmsSource.R xcms/R/zzz.R
xcms/build
xcms/build/vignette.rds
xcms/inst
xcms/inst/CHANGELOG
xcms/inst/CITATION
xcms/inst/NEWS
xcms/inst/doc
xcms/inst/doc/xcmsDirect.R
xcms/inst/doc/xcmsDirect.Rnw
xcms/inst/doc/xcmsDirect.pdf
xcms/inst/doc/xcmsInstall.Rnw
xcms/inst/doc/xcmsInstall.pdf
xcms/inst/doc/xcmsMSn.R
xcms/inst/doc/xcmsMSn.Rnw
xcms/inst/doc/xcmsMSn.pdf
xcms/inst/doc/xcmsPreprocess.R
xcms/inst/doc/xcmsPreprocess.Rnw
xcms/inst/doc/xcmsPreprocess.pdf
xcms/inst/unitTests
xcms/inst/unitTests/Makefile
xcms/inst/unitTests/mzQuantML_1_0_0.xsd
xcms/inst/unitTests/runit.BiocParallel.R
xcms/inst/unitTests/runit.absentPresent.R
xcms/inst/unitTests/runit.diffreport.R
xcms/inst/unitTests/runit.fillPeaks.R
xcms/inst/unitTests/runit.findPeaksCentWave.R
xcms/inst/unitTests/runit.findPeaksCentWave.fitGauss.plot.R
xcms/inst/unitTests/runit.findPeaksCentWaveWithIsotopeROIs.R
xcms/inst/unitTests/runit.findPeaksMassIfQuant.R
xcms/inst/unitTests/runit.getEIC.R
xcms/inst/unitTests/runit.getXcmsRaw.R
xcms/inst/unitTests/runit.group.R
xcms/inst/unitTests/runit.msms.R
xcms/inst/unitTests/runit.obiwarp.R
xcms/inst/unitTests/runit.phenoData.R
xcms/inst/unitTests/runit.ramp.R
xcms/inst/unitTests/runit.rawMat.R
xcms/inst/unitTests/runit.sampclass.R
xcms/inst/unitTests/runit.scanrage.R
xcms/inst/unitTests/runit.snames.R
xcms/inst/unitTests/runit.specDist.R
xcms/inst/unitTests/runit.splitCombine.R
xcms/inst/unitTests/runit.splitRaw.R
xcms/inst/unitTests/runit.unusedGroups.R
xcms/inst/unitTests/runit.writecdf.R
xcms/inst/unitTests/runit.writemzdata.R
xcms/inst/unitTests/runit.writemzquantml.R
xcms/inst/unitTests/runit.xcmsRawCopy.R
xcms/inst/unitTests/runit.xcmsSet.R
xcms/inst/unitTests/test_binning.R
xcms/inst/unitTests/test_do_detectFeatures_centWave.R
xcms/inst/unitTests/test_do_detectFeatures_matchedFilter.R
xcms/inst/unitTests/test_updateObject.R
xcms/man
xcms/man/AutoLockMass-methods.Rd xcms/man/SSgauss.Rd xcms/man/absent-methods.Rd xcms/man/c.xcmsSet.Rd xcms/man/calibrate.Rd xcms/man/colMax.Rd xcms/man/collect-methods.Rd xcms/man/descendZero.Rd xcms/man/diffreport-methods.Rd xcms/man/doubleMatrix.Rd xcms/man/etg.Rd xcms/man/fillPeaks-methods.Rd xcms/man/fillPeaks.MSW-methods.Rd xcms/man/fillPeaks.chrom-methods.Rd xcms/man/filtfft.Rd xcms/man/findEqualGreater.Rd xcms/man/findMZ.Rd xcms/man/findPeaks-methods.Rd xcms/man/findPeaks.MS1-methods.Rd xcms/man/findPeaks.MSW-methods.Rd xcms/man/findPeaks.addPredictedIsotopeFeatures-methods.Rd xcms/man/findPeaks.centWave-methods.Rd xcms/man/findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd xcms/man/findPeaks.massifquant-methods.Rd xcms/man/findPeaks.matchedFilter-methods.Rd xcms/man/findneutral.Rd xcms/man/getEIC-methods.Rd xcms/man/getPeaks-methods.Rd xcms/man/getScan-methods.Rd xcms/man/getSpec-methods.Rd xcms/man/getXcmsRaw-methods.Rd xcms/man/group-methods.Rd xcms/man/group.density.Rd xcms/man/group.mzClust.Rd xcms/man/group.nearest.Rd xcms/man/groupnames-methods.Rd xcms/man/groupval-methods.Rd xcms/man/image.xcmsRaw.Rd xcms/man/levelplot.xcmsRaw.Rd xcms/man/loadRaw-methods.Rd xcms/man/medianFilter.Rd xcms/man/msn2xcmsRaw.Rd xcms/man/na.flatfill.Rd xcms/man/netCDF.Rd xcms/man/netCdfSource-class.Rd xcms/man/panel.cor.Rd xcms/man/peakPlots-methods.Rd xcms/man/peakTable-methods.Rd xcms/man/plot.xcmsEIC.Rd xcms/man/plotChrom-methods.Rd xcms/man/plotEIC-methods.Rd xcms/man/plotPeaks-methods.Rd xcms/man/plotQC.Rd xcms/man/plotRaw-methods.Rd xcms/man/plotScan-methods.Rd xcms/man/plotSpec-methods.Rd xcms/man/plotSurf-methods.Rd xcms/man/plotTIC-methods.Rd xcms/man/plotrt-methods.Rd xcms/man/profGenerate.Rd xcms/man/profMedFilt-methods.Rd xcms/man/profMethod-methods.Rd xcms/man/profRange-methods.Rd xcms/man/profStep-methods.Rd xcms/man/pval.Rd xcms/man/rampSource-class.Rd xcms/man/rawEIC-methods.Rd xcms/man/rawMat-methods.Rd xcms/man/rectUnique.Rd xcms/man/retcor-methods.Rd xcms/man/retcor.obiwarp-methods.Rd xcms/man/retcor.peakgroups-methods.Rd xcms/man/retexp.Rd xcms/man/sampnames-methods.Rd xcms/man/specDist-methods.Rd xcms/man/specDist.cosine-methods.Rd xcms/man/specDist.meanMZmatch-methods.Rd xcms/man/specDist.peakCount-methods.Rd xcms/man/specNoise.Rd xcms/man/specPeaks.Rd xcms/man/split.xcmsRaw.Rd xcms/man/split.xcmsSet.Rd xcms/man/stitch-methods.Rd xcms/man/updateObject-xcmsSet-method.Rd xcms/man/valueCount2ScanIndex.Rd xcms/man/verify.mzQuantML.Rd xcms/man/write.cdf-methods.Rd xcms/man/write.mzQuantML.Rd xcms/man/write.mzdata-methods.Rd xcms/man/writeMzTab.Rd xcms/man/xcms-deprecated.Rd xcms/man/xcmsEIC-class.Rd xcms/man/xcmsFileSource-class.Rd xcms/man/xcmsFragments-class.Rd xcms/man/xcmsFragments.Rd xcms/man/xcmsPapply.Rd xcms/man/xcmsPeaks-class.Rd xcms/man/xcmsRaw-class.Rd xcms/man/xcmsRaw.Rd xcms/man/xcmsSet-class.Rd xcms/man/xcmsSet.Rd xcms/man/xcmsSource-class.Rd xcms/man/xcmsSource-methods.Rd
xcms/readme.org
xcms/src
xcms/src/Makevars
xcms/src/Makevars.win
xcms/src/binarySearch.h
xcms/src/binners.c
xcms/src/binners.h
xcms/src/fastMatch.c
xcms/src/massifquant
xcms/src/massifquant/DataKeeper.cpp
xcms/src/massifquant/DataKeeper.h
xcms/src/massifquant/OpOverload.cpp
xcms/src/massifquant/OpOverload.h
xcms/src/massifquant/SegProc.cpp
xcms/src/massifquant/SegProc.h
xcms/src/massifquant/TrMgr.cpp
xcms/src/massifquant/TrMgr.h
xcms/src/massifquant/Tracker.cpp
xcms/src/massifquant/Tracker.h
xcms/src/massifquant/dpq.h
xcms/src/massifquant/nmath.h
xcms/src/massifquant/xcms_massifquant.cpp
xcms/src/mzClust_hclust.c
xcms/src/mzROI.c
xcms/src/obiwarp
xcms/src/obiwarp/lmat.h
xcms/src/obiwarp/mat.cpp
xcms/src/obiwarp/mat.h
xcms/src/obiwarp/vec.cpp
xcms/src/obiwarp/vec.h
xcms/src/obiwarp/xcms_dynprog.cpp
xcms/src/obiwarp/xcms_dynprog.h
xcms/src/obiwarp/xcms_lmat.cpp
xcms/src/util.c
xcms/src/util.h
xcms/src/win
xcms/src/win/i386
xcms/src/win/x64
xcms/src/xcms.c
xcms/src/xcms.h
xcms/src/xcms_obiwarp.cpp
xcms/tests
xcms/tests/doRUnit.R
xcms/vignettes
xcms/vignettes/FlowChart.graffle
xcms/vignettes/FlowChart.pdf
xcms/vignettes/benchmarking.Rmd-disabled
xcms/vignettes/new_functionality.org
xcms/vignettes/xcms.bib
xcms/vignettes/xcmsDirect.Rnw
xcms/vignettes/xcmsInstall.Rnw
xcms/vignettes/xcmsMSn.Rnw
xcms/vignettes/xcmsPreprocess.Rnw

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