LC/MS and GC/MS Data Analysis


[Package List] [Top]

Documentation for package ‘xcms’ version 1.14.1

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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

-- C --

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

-- D --

diffreport Create report of analyte differences
diffreport,xcmsSet-method Create report of analyte differences

-- E --

etg Empirically Transformed Gaussian function

-- F --

filepaths Class xcmsSet, a class for preprocessing peak data
filepaths,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
filepaths<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
fillPeaks Integrate areas of missing peaks
fillPeaks,xcmsSet-method Integrate areas of missing peaks
findPeaks Feature detection for GC/MS and LC/MS Data - methods
findPeaks,xcmsRaw-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,xcmsRaw-method Feature detection for high resolution LC/MS data
findPeaks.matchedFilter Feature detection in the chromatographic time domain
findPeaks.matchedFilter,xcmsRaw-method Feature detection in the chromatographic time domain
findPeaks.MS1 Collecting MS1 precursor peaks
findPeaks.MS1,xcmsRaw-method Collecting MS1 precursor peaks
findPeaks.MSW Feature detection for single-spectrum non-chromatography MS data
findPeaks.MSW,xcmsRaw-method Feature detection for single-spectrum non-chromatography MS data

-- G --

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

-- I --

image, image-methods Plot log intensity image of a xcmsRaw object
image.xcmsRaw Plot log intensity image of a xcmsRaw object

-- M --

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

-- P --

peaks Class xcmsSet, a class for preprocessing peak data
peaks,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
peaks<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
phenoData Class xcmsSet, a class for preprocessing peak data
phenoData,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
phenoData<-,xcmsSet-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,xcmsRaw-method Plot extracted ion chromatograms from the profile matrix
plotPeaks Plot a grid of a large number of peaks
plotPeaks,xcmsRaw-method Plot a grid of a large number of peaks
plotRaw Scatterplot of raw data points
plotRaw,xcmsRaw-method Scatterplot of raw data points
plotrt Plot retention time deviation profiles
plotrt,xcmsSet-method Plot retention time deviation profiles
plotScan Plot a single mass scan
plotScan,xcmsRaw-method Plot a single mass scan
plotSpec Plot mass spectra from the profile matrix
plotSpec,xcmsRaw-method Plot mass spectra from the profile matrix
plotSurf Plot profile matrix 3D surface using OpenGL
plotSurf,xcmsRaw-method Plot profile matrix 3D surface using OpenGL
plotTIC Plot total ion count
plotTIC,xcmsRaw-method Plot total ion count
plotTree Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
plotTree,xcmsFragments-method Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
profinfo Class xcmsSet, a class for preprocessing peak data
profinfo,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
profinfo<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
profMedFilt Median filtering of the profile matrix
profMedFilt,xcmsRaw-method Median filtering of the profile matrix
profMethod Get and set method for generating profile data
profMethod,xcmsRaw-method Get and set method for generating profile data
profMethod<-,xcmsRaw-method Get and set method for generating profile data
profMz Class xcmsRaw, a class for handling raw data
profMz,xcmsRaw-method Class xcmsRaw, a class for handling raw data
profRange Specify a subset of profile mode data
profRange,xcmsRaw-method Specify a subset of profile mode data
profStep Get and set m/z step for generating profile data
profStep,xcmsRaw-method Get and set m/z step for generating profile data
profStep<-,xcmsRaw-method Get and set m/z step for generating profile data

-- R --

rawEIC Get extracted ion chromatograms for specified m/z range
rawEIC,xcmsRaw-method Get extracted ion chromatograms for specified m/z range
retcor Align retention times across samples
retcor,xcmsSet-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,xcmsRaw-method Class xcmsRaw, a class for handling raw data
rtrange Class xcmsEIC, a class for multi-sample extracted ion chromatograms
rtrange,xcmsEIC-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms

-- S --

sampclass Class xcmsSet, a class for preprocessing peak data
sampclass,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
sampclass<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
sampnames Get sample names
sampnames,xcmsEIC-method Get sample names
sampnames,xcmsSet-method Get sample names
sampnames<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
score_fun Scoring for MS/MS spectra
searchMetlin Search Metlin Online Database
searchMetlin,xcmsFragments-method Search Metlin Online Database
show,xcmsEIC-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms
show,xcmsFragments-method Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
show,xcmsRaw-method Class xcmsRaw, a class for handling raw data
show,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
simSearch Unrestricted precursor Metlin Search
simSearch,xcmsFragments-method Unrestricted precursor Metlin Search
sortMz Class xcmsRaw, a class for handling raw data
sortMz,xcmsRaw-method Class xcmsRaw, a class for handling raw data
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.xcmsSet Divide an xcmsSet object
SSgauss Gaussian Model

-- W --

write.cdf Save an xcmsRaw object to file
write.cdf,xcmsRaw-method Save an xcmsRaw object to 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
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