LC/MS and GC/MS Data Analysis

Documentation for package ‘xcms’ version 1.26.1

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.
Package NEWS.

Help Pages

-- A --

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

-- C --

c, c-methods	Combine xcmsSet objects
c.xcmsSet	Combine xcmsSet objects
calibrate	Calibrate peaks for correcting unprecise m/z values
calibrate-method	Calibrate peaks for correcting unprecise m/z values
collect	Collect MS^n peaks into xcmsFragments
collect-method	Collect MS^n peaks into xcmsFragments
collect-methods	Collect MS^n peaks into xcmsFragments

-- D --

deepCopy	Constructor for xcmsRaw objects which reads NetCDF/mzXML files
deepCopy-method	Constructor for xcmsRaw objects which reads NetCDF/mzXML files
diffreport	Create report of analyte differences
diffreport-method	Create report of analyte differences

-- E --

etg	Empirically Transformed Gaussian function

-- F --

filepaths	Class xcmsSet, a class for preprocessing peak data
filepaths-method	Class xcmsSet, a class for preprocessing peak data
filepaths<-	Class xcmsSet, a class for preprocessing peak data
filepaths<--method	Class xcmsSet, a class for preprocessing peak data
fillPeaks	Integrate areas of missing peaks
fillPeaks-method	Integrate areas of missing peaks
fillPeaks.chrom	Integrate areas of missing peaks
fillPeaks.chrom-method	Integrate areas of missing peaks
fillPeaks.MSW	Integrate areas of missing peaks in FTICR-MS data
fillPeaks.MSW-method	Integrate areas of missing peaks in FTICR-MS data
findMZ	Find fragment ions in xcmsFragment objects
findMZ-method	Find fragment ions in xcmsFragment objects
findneutral	Find neutral losses in xcmsFragment objects
findneutral-method	Find neutral losses in xcmsFragment objects
findPeaks	Feature detection for GC/MS and LC/MS Data - methods
findPeaks-method	Feature detection for GC/MS and LC/MS Data - methods
findPeaks-methods	Feature detection for GC/MS and LC/MS Data - methods
findPeaks.centWave	Feature detection for high resolution LC/MS data
findPeaks.centWave-method	Feature detection for high resolution LC/MS data
findPeaks.matchedFilter	Feature detection in the chromatographic time domain
findPeaks.matchedFilter-method	Feature detection in the chromatographic time domain
findPeaks.MS1	Collecting MS1 precursor peaks
findPeaks.MS1-method	Collecting MS1 precursor peaks
findPeaks.MSW	Feature detection for single-spectrum non-chromatography MS data
findPeaks.MSW-method	Feature detection for single-spectrum non-chromatography MS data

-- G --

getEIC	Get extracted ion chromatograms for specified m/z ranges
getEIC-method	Get extracted ion chromatograms for specified m/z ranges
getPeaks	Get peak intensities for specified regions
getPeaks-method	Get peak intensities for specified regions
getScan	Get m/z and intensity values for a single mass scan
getScan-method	Get m/z and intensity values for a single mass scan
getSpec	Get average m/z and intensity values for multiple mass scans
getSpec-method	Get average m/z and intensity values for multiple mass scans
group	Group peaks from different samples together
group-method	Group peaks from different samples together
group-methods	Group peaks from different samples together
group.density	Group peaks from different samples together
group.density-method	Group peaks from different samples together
group.mzClust	Group Peaks via High Resolution Alignment
group.mzClust-method	Group Peaks via High Resolution Alignment
group.nearest	Group peaks from different samples together
group.nearest-method	Group peaks from different samples together
groupidx	Class xcmsSet, a class for preprocessing peak data
groupidx-method	Class xcmsSet, a class for preprocessing peak data
groupidx<-	Class xcmsSet, a class for preprocessing peak data
groupidx<--method	Class xcmsSet, a class for preprocessing peak data
groupnames	Generate unque names for peak groups
groupnames-method	Generate unque names for peak groups
groups	Class xcmsSet, a class for preprocessing peak data
groups-method	Class xcmsSet, a class for preprocessing peak data
groups<-	Class xcmsSet, a class for preprocessing peak data
groups<--method	Class xcmsSet, a class for preprocessing peak data
groupval	Extract a matrix of peak values for each group
groupval-method	Extract a matrix of peak values for each group

-- I --

image-method

Plot log intensity image of a xcmsRaw object

-- M --

makeacqNum	Correct gaps in data
makeacqNum-method	Correct gaps in data
medianFilter	Apply a median filter to a matrix
mzrange	Class xcmsEIC, a class for multi-sample extracted ion chromatograms
mzrange-method	Class xcmsEIC, a class for multi-sample extracted ion chromatograms

-- P --

peakPlots-method	Plot a grid of a large number of peaks
peakPlots-methods	Plot a grid of a large number of peaks
peaks	Class xcmsSet, a class for preprocessing peak data
peaks-method	Class xcmsSet, a class for preprocessing peak data
peaks<-	Class xcmsSet, a class for preprocessing peak data
peaks<--method	Class xcmsSet, a class for preprocessing peak data
peakTable	Create report of aligned peak intensities
peakTable-method	Create report of aligned peak intensities
phenoData	Class xcmsSet, a class for preprocessing peak data
phenoData-method	Class xcmsSet, a class for preprocessing peak data
phenoData<-	Class xcmsSet, a class for preprocessing peak data
phenoData<--method	Class xcmsSet, a class for preprocessing peak data
plot, plot-methods	Plot extracted ion chromatograms from multiple files
plot.xcmsEIC	Plot extracted ion chromatograms from multiple files
plotChrom	Plot extracted ion chromatograms from the profile matrix
plotChrom-method	Plot extracted ion chromatograms from the profile matrix
plotEIC	Plot extracted ion chromatograms for specified m/z range
plotEIC-method	Plot extracted ion chromatograms for specified m/z range
plotPeaks	Plot a grid of a large number of peaks
plotPeaks-method	Plot a grid of a large number of peaks
plotRaw	Scatterplot of raw data points
plotRaw-method	Scatterplot of raw data points
plotrt	Plot retention time deviation profiles
plotrt-method	Plot retention time deviation profiles
plotScan	Plot a single mass scan
plotScan-method	Plot a single mass scan
plotSpec	Plot mass spectra from the profile matrix
plotSpec-method	Plot mass spectra from the profile matrix
plotSurf	Plot profile matrix 3D surface using OpenGL
plotSurf-method	Plot profile matrix 3D surface using OpenGL
plotTIC	Plot total ion count
plotTIC-method	Plot total ion count
plotTree	Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
plotTree-method	Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
present	Determine which peaks are absent / present in a sample class
present-method	Determine which peaks are absent / present in a sample class
profinfo	Class xcmsSet, a class for preprocessing peak data
profinfo-method	Class xcmsSet, a class for preprocessing peak data
profinfo<-	Class xcmsSet, a class for preprocessing peak data
profinfo<--method	Class xcmsSet, a class for preprocessing peak data
profMedFilt	Median filtering of the profile matrix
profMedFilt-method	Median filtering of the profile matrix
profMethod	Get and set method for generating profile data
profMethod-method	Get and set method for generating profile data
profMethod<-	Get and set method for generating profile data
profMethod<--method	Get and set method for generating profile data
profMz	Class xcmsRaw, a class for handling raw data
profMz-method	Class xcmsRaw, a class for handling raw data
profRange	Specify a subset of profile mode data
profRange-method	Specify a subset of profile mode data
profStep	Get and set m/z step for generating profile data
profStep-method	Get and set m/z step for generating profile data
profStep<-	Get and set m/z step for generating profile data
profStep<--method	Get and set m/z step for generating profile data
progressCallback	Class xcmsSet, a class for preprocessing peak data
progressCallback-method	Class xcmsSet, a class for preprocessing peak data
progressCallback<-	Class xcmsSet, a class for preprocessing peak data
progressCallback<--method	Class xcmsSet, a class for preprocessing peak data

-- R --

rawEIC	Get extracted ion chromatograms for specified m/z range
rawEIC-method	Get extracted ion chromatograms for specified m/z range
rawMat	Get a raw data matrix
rawMat-method	Get a raw data matrix
rawMat-methods	Get a raw data matrix
retcor	Correct retention time from different samples
retcor-method	Correct retention time from different samples
retcor-methods	Correct retention time from different samples
retcor.linear	Align retention times across samples
retcor.linear-method	Align retention times across samples
retcor.loess	Align retention times across samples
retcor.loess-method	Align retention times across samples
retcor.obiwarp	Align retention times across samples with Obiwarp
retcor.obiwarp-method	Align retention times across samples with Obiwarp
retcor.peakgroups	Align retention times across samples
retcor.peakgroups-method	Align retention times across samples
retexp	Set retention time window to a specified width
revMz	Class xcmsRaw, a class for handling raw data
revMz-method	Class xcmsRaw, a class for handling raw data
rtrange	Class xcmsEIC, a class for multi-sample extracted ion chromatograms
rtrange-method	Class xcmsEIC, a class for multi-sample extracted ion chromatograms

-- S --

sampclass	Class xcmsSet, a class for preprocessing peak data
sampclass-method	Class xcmsSet, a class for preprocessing peak data
sampclass<-	Class xcmsSet, a class for preprocessing peak data
sampclass<--method	Class xcmsSet, a class for preprocessing peak data
sampnames	Get sample names
sampnames-method	Get sample names
sampnames<-	Class xcmsSet, a class for preprocessing peak data
sampnames<--method	Class xcmsSet, a class for preprocessing peak data
score_fun	Scoring for MS/MS spectra
score_fun.cor	Scoring for MS/MS spectra Via correlation
score_fun.distMatrix	Scoring for MS/MS spectra
searchMetlin	Search Metlin Online Database
searchMetlin-method	Search Metlin Online Database
show-method	Class xcmsEIC, a class for multi-sample extracted ion chromatograms
show-method	Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
show-method	A matrix of peaks
show-method	Class xcmsRaw, a class for handling raw data
show-method	Class xcmsSet, a class for preprocessing peak data
simSearch	Unrestricted precursor Metlin Search
simSearch-method	Unrestricted precursor Metlin Search
sortMz	Class xcmsRaw, a class for handling raw data
sortMz-method	Class xcmsRaw, a class for handling raw data
specDist	Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-method	Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist-methods	Distance methods for xcmsSet, xcmsRaw and xsAnnotate
specDist.cosine	a Distance function based on matching peaks
specDist.cosine-method	a Distance function based on matching peaks
specDist.meanMZmatch	a Distance function based on matching peaks
specDist.meanMZmatch-method	a Distance function based on matching peaks
specDist.peakCount	a Distance function based on matching peaks
specDist.peakCount-method	a Distance function based on matching peaks
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, split-methods	Divide an xcmsSet object
split.xcmsRaw	Divide an xcmsRaw object
split.xcmsSet	Divide an xcmsSet object
SSgauss	Gaussian Model
stitch	Correct gaps in data
stitch-method	Correct gaps in data
stitch-methods	Correct gaps in data

-- W --

write.cdf	Save an xcmsRaw object to file
write.cdf-method	Save an xcmsRaw object to file
write.mzdata	Save an xcmsRaw object to a file
write.mzdata-method	Save an xcmsRaw object to a file

-- X --

xcmsEIC-class	Class xcmsEIC, a class for multi-sample extracted ion chromatograms
xcmsFragments	Constructor for xcmsFragments objects which holds Tandem MS peaks
xcmsFragments-class	Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
xcmsPapply	xcmsPapply
xcmsPeaks-class	A matrix of peaks
xcmsRaw	Constructor for xcmsRaw objects which reads NetCDF/mzXML files
xcmsRaw-class	Class xcmsRaw, a class for handling raw data
xcmsSet	Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files
xcmsSet-class	Class xcmsSet, a class for preprocessing peak data