LC/MS and GC/MS Data Analysis

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Documentation for package ‘xcms’ version 1.44.0

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A C D E F G I L M P R S V W X

-- A --

absent Determine which peaks are absent / present in a sample class
absent-method Determine which peaks are absent / present in a sample class
AutoLockMass Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-method Automatic parameter for Lock mass fixing 'AutoLockMass' ~~
AutoLockMass-methods Automatic parameter for Lock mass fixing 'AutoLockMass' ~~

-- 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.massifquant Feature detection for XC-MS data.
findPeaks.massifquant-method Feature detection for XC-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
getMsnScan Get m/z and intensity values for a single mass scan
getMsnScan-method Get m/z and intensity values for a single mass scan
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

-- L --

loadRaw Read binary data from a source
loadRaw-method Read binary data from a source
loadRaw-methods Read binary data from a source

-- M --

makeacqNum Correct gaps in data
makeacqNum-method Correct gaps in data
medianFilter Apply a median filter to a matrix
msn2xcmsRaw Copy MSn data in an xcmsRaw to the MS slots
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
plotQC Plot m/z and RT deviations for QC purposes without external reference data
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
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
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
stitch.netCDF Correct gaps in data
stitch.xml Correct gaps in data

-- V --

verify.mzQuantML Verify an mzQuantML file

-- 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
write.mzQuantML Save an xcmsSet object to an PSI mzQuantML file
write.mzQuantML-method Save an xcmsSet object to an PSI mzQuantML file

-- X --

xcmsEIC-class Class xcmsEIC, a class for multi-sample extracted ion chromatograms
xcmsFileSource-class Base class for loading raw data from a file
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
xcmsSource Create an 'xcmsSource' object in a flexible way
xcmsSource-class Virtual class for raw data sources
xcmsSource-method Base class for loading raw data from a file
xcmsSource-method Create an 'xcmsSource' object in a flexible way
xcmsSource-methods Create an 'xcmsSource' object in a flexible way