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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 |