getEIC |
Get extracted ion chromatograms for specified m/z ranges |
getEIC-method |
Get extracted ion chromatograms for specified m/z ranges |
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 |
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 |
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 |
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 |