c.xcmsSet | Combine xcmsSet objects |
cdfpaths | Class xcmsSet, a class for preprocessing peak data |
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 |
groupnames | Generate unque names for peak groups |
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 |
mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
peaks | 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 |
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 |
rtrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
sampclass | Class xcmsSet, a class for preprocessing peak data |
sampnames | Get sample names |
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 |
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 |