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.

Author
Colin 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 publication
None
Maintainer
Steffen Neumann <sneumann@ipb-halle.de>
License
GPL (>= 2) + file LICENSE
Version
1.50.0
URLs

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