# LC/MS and GC/MS Data Analysis

## Documentation for package `xcms' version 1.6.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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