LC/MS and GC/MS Data Analysis


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Documentation for package `xcms' version 1.0.0

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c.xcmsSet Combine xcmsSet objects
cdfpaths Class xcmsSet, a class for preprocessing peak data
colMax Find row and column maximum values
diffreport Create report of analyte differences
etg Empirically Transformed Gaussian function
fillPeaks Integrate areas of missing peaks
findPeaks Feature detection in the chromatographic time domain
getEIC Get extracted ion chromatograms for specified m/z ranges
getPeaks Get peak intensities for specified regions
getScan Get m/z and intensity values for a single mass scan
getSpec Get average m/z and intensity values for multiple mass scans
group Group peaks from different samples together
groupidx Class xcmsSet, a class for preprocessing peak data
groups Class xcmsSet, a class for preprocessing peak data
groupval Extract a matrix of peak values for each group
image.xcmsRaw Plot log intensity image of a xcmsRaw object
medianFilter Apply a median filter to a matrix
peaks Class xcmsSet, a class for preprocessing peak data
plotChrom Plot extracted ion chromatograms from the profile matrix
plotEIC Plot a list of EICs for each sample
plotPeaks Plot a grid of a large number of peaks
plotRaw Scatterplot of raw data points
plotrt Plot retention time deviation profiles
plotScan Plot a single mass scan
plotSpec Plot mass spectra from the profile matrix
plotSurf Plot profile matrix 3D surface using OpenGL
plotTIC Plot total ion count
profinfo Class xcmsSet, a class for preprocessing peak data
profMedFilt Apply a median filter to the profile matrix
profMethod Get and set method for generating profile data
profMz Class xcmsRaw, a class for handling raw data
profRange Specify a subset of profile mode data
profStep Get and set m/z step for generating profile data
retcor Align retention times across samples
retexp Set retention time window to a specified width
revMz Class xcmsRaw, a class for handling raw data
rowMax Find row and column maximum values
sampclass Class xcmsSet, a class for preprocessing peak data
sampnames Class xcmsSet, a class for preprocessing peak data
sortMz 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
xcmsRaw Constructor for xcmsRaw objects which reads NetCDF files
xcmsRaw-class Class xcmsRaw, a class for handling raw data
xcmsSet Constructor for xcmsSet objects which finds peaks in NetCDF files
xcmsSet-class Class xcmsSet, a class for preprocessing peak data