LC/MS and GC/MS Data Analysis


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Documentation for package `xcms' version 1.6.1

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C D E F G I M P R S X

-- C --

c.xcmsSet Combine xcmsSet objects
cdfpaths Class xcmsSet, a class for preprocessing peak data
cdfpaths,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
cdfpaths<-,xcmsSet-method Class xcmsSet, a class for preprocessing peak data

-- D --

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

-- E --

etg Empirically Transformed Gaussian function

-- F --

fillPeaks Integrate areas of missing peaks
fillPeaks,xcmsSet-method Integrate areas of missing peaks
findPeaks Feature detection in the chromatographic time domain
findPeaks,xcmsRaw-method Feature detection in the chromatographic time domain

-- 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
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.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
plot Plot extracted ion chromatograms from multiple files
plot,xcmsEIC-method 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
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 Apply a median filter to the profile matrix
profMedFilt,xcmsRaw-method Apply a median filter to 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 --

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
show,xcmsEIC-method Class xcmsEIC, a class for multi-sample extracted ion chromatograms
show,xcmsRaw-method Class xcmsRaw, a class for handling raw data
show,xcmsSet-method Class xcmsSet, a class for preprocessing peak data
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.xcmsSet Divide an xcmsSet object
SSgauss Gaussian Model

-- X --

xcmsEIC-class Class xcmsEIC, a class for multi-sample extracted ion chromatograms
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