| absent-methods | Determine which peaks are absent / present in a sample class |
| AutoLockMass-methods | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
| calibrate | Calibrate peaks for correcting unprecise m/z values |
| collect-methods | Collect MS^n peaks into xcmsFragments |
| colMax | Find row and column maximum values |
| c.xcmsSet | Combine xcmsSet objects |
| descendZero | Find start and end points of a peak |
| diffreport-methods | Create report of analyte differences |
| doubleMatrix | Allocate double, integer, or logical matricies |
| etg | Empirically Transformed Gaussian function |
| fillPeaks.chrom-methods | Integrate areas of missing peaks |
| fillPeaks-methods | Integrate areas of missing peaks |
| fillPeaks.MSW-methods | Integrate areas of missing peaks in FTICR-MS data |
| filtfft | Apply an convolution filter using an FFT |
| findEqualGreater | Find values in sorted vectors |
| findMZ | Find fragment ions in xcmsFragment objects |
| findneutral | Find neutral losses in xcmsFragment objects |
| findPeaks.centWave-methods | Feature detection for high resolution LC/MS data |
| findPeaks.massifquant-methods | Feature detection for XC-MS data. |
| findPeaks.matchedFilter-methods | Feature detection in the chromatographic time domain |
| findPeaks-methods | Feature detection for GC/MS and LC/MS Data - methods |
| findPeaks.MS1-methods | Collecting MS1 precursor peaks |
| findPeaks.MSW-methods | Feature detection for single-spectrum non-chromatography MS... |
| getEIC-methods | Get extracted ion chromatograms for specified m/z ranges |
| getPeaks-methods | Get peak intensities for specified regions |
| getScan-methods | Get m/z and intensity values for a single mass scan |
| getSpec-methods | Get average m/z and intensity values for multiple mass scans |
| group.density | Group peaks from different samples together |
| group-methods | Group peaks from different samples together |
| group.mzClust | Group Peaks via High Resolution Alignment |
| groupnames-methods | Generate unque names for peak groups |
| group.nearest | Group peaks from different samples together |
| groupval-methods | Extract a matrix of peak values for each group |
| image.xcmsRaw | Plot log intensity image of a xcmsRaw object |
| loadRaw-methods | Read binary data from a source |
| medianFilter | Apply a median filter to a matrix |
| msn2xcmsRaw | Copy MSn data in an xcmsRaw to the MS slots |
| na.flatfill | Fill in NA values at the extremes of a vector |
| netCDF | High-performance, low-level access to NetCDF data files |
| netCdfSource-class | Class '"netCdfSource"', for reading raw data from 'netCDF'... |
| panel.cor | Correlation coefficient panel for pairs function |
| peakPlots-methods | Plot a grid of a large number of peaks |
| peakTable-methods | Create report of aligned peak intensities |
| plotChrom-methods | Plot extracted ion chromatograms from the profile matrix |
| plotEIC-methods | Plot extracted ion chromatograms for specified m/z range |
| plotPeaks-methods | Plot a grid of a large number of peaks |
| plotRaw-methods | Scatterplot of raw data points |
| plotrt-methods | Plot retention time deviation profiles |
| plotScan-methods | Plot a single mass scan |
| plotSpec-methods | Plot mass spectra from the profile matrix |
| plotSurf-methods | Plot profile matrix 3D surface using OpenGL |
| plotTIC-methods | Plot total ion count |
| plot.xcmsEIC | Plot extracted ion chromatograms from multiple files |
| profGenerate | Generation of profile data |
| profMedFilt-methods | Median filtering of the profile matrix |
| profMethod-methods | Get and set method for generating profile data |
| profRange-methods | Specify a subset of profile mode data |
| profStep-methods | Get and set m/z step for generating profile data |
| pval | Generate p-values for a vector of t-statistics |
| ramp | High-performance, low-level access to mzXML/mzData files |
| rampSource-class | Class '"rampSource"', for reading raw data from 'netCDF'... |
| rawEIC-methods | Get extracted ion chromatograms for specified m/z range |
| rawMat-methods | Get a raw data matrix |
| rectUnique | Determine a subset of rectangles with unique, non-overlapping... |
| retcor-methods | Correct retention time from different samples |
| retcor.obiwarp-methods | Align retention times across samples with Obiwarp |
| retcor.peakgroups-methods | Align retention times across samples |
| retexp | Set retention time window to a specified width |
| sampnames-methods | Get sample names |
| specDist.cosine-methods | a Distance function based on matching peaks |
| specDist.meanMZmatch-methods | a Distance function based on matching peaks |
| specDist-methods | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
| 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.xcmsRaw | Divide an xcmsRaw object |
| split.xcmsSet | Divide an xcmsSet object |
| SSgauss | Gaussian Model |
| stitch-methods | Correct gaps in data |
| verify.mzQuantML | Verify an mzQuantML file |
| write.cdf-methods | Save an xcmsRaw object to file |
| write.mzdata-methods | Save an xcmsRaw object to a file |
| write.mzQuantML | Save an xcmsSet object to an PSI mzQuantML file |
| xcmsEIC-class | Class xcmsEIC, a class for multi-sample extracted ion... |
| xcmsFileSource-class | Base class for loading raw data from a file |
| xcmsFragments | Constructor for xcmsFragments objects which holds Tandem MS... |
| xcmsFragments-class | Class xcmsFragments, a class for handling Tandem MS and... |
| xcmsPapply | xcmsPapply |
| xcmsPeaks-class | A matrix of peaks |
| xcmsRaw | Constructor for xcmsRaw objects which reads NetCDF/mzXML... |
| xcmsRaw-class | Class xcmsRaw, a class for handling raw data |
| xcmsSet | Constructor for xcmsSet objects which finds peaks in... |
| xcmsSet-class | Class xcmsSet, a class for preprocessing peak data |
| xcmsSource-class | Virtual class for raw data sources |
| xcmsSource-methods | Create an 'xcmsSource' object in a flexible way |
