Man pages for sneumann/xcms
LC-MS and GC-MS Data Analysis
| absent-methods | Determine which peaks are absent / present in a sample class |
| adjustRtime | Alignment: Retention time correction methods. |
| applyAdjustedRtime | Replace raw with adjusted retention times |
| AutoLockMass-methods | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
| binYonX | Aggregate values in y for bins defined on x |
| BlankFlag | Flag features based on the intensity in blank samples |
| breaks_on_binSize | Generate breaks for binning using a defined bin size. |
| breaks_on_nBins | Generate breaks for binning |
| calibrate | Calibrate peaks for correcting unprecise m/z values |
| calibrate-calibrant-mass | Calibrant mass based calibration of chromatgraphic peaks |
| chromatogram-method | Extracting chromatograms |
| chromPeakChromatograms | Extract an ion chromatogram for each chromatographic peak |
| chromPeakSpectra | Extract spectra associated with chromatographic peaks |
| collect-methods | Collect MS^n peaks into xcmsFragments |
| colMax | Find row and column maximum values |
| correlate-Chromatogram | Correlate chromatograms |
| c.xcmsSet | Combine xcmsSet objects |
| descendZero | Find start and end points of a peak |
| diffreport-methods | Create report of analyte differences |
| dirname | Change the file path of an 'OnDiskMSnExp' object |
| do_adjustRtime_peakGroups | Align spectrum retention times across samples using peak... |
| do_findChromPeaks_centWave | Core API function for centWave peak detection |
| do_findChromPeaks_centWaveWithPredIsoROIs | Core API function for two-step centWave peak detection with... |
| do_findChromPeaks_massifquant | Core API function for massifquant peak detection |
| do_findChromPeaks_matchedFilter | Core API function for matchedFilter peak detection |
| do_findPeaks_MSW | Core API function for single-spectrum non-chromatography MS... |
| do_groupChromPeaks_density | Core API function for peak density based chromatographic peak... |
| do_groupChromPeaks_nearest | Core API function for chromatic peak grouping using a nearest... |
| do_groupPeaks_mzClust | Core API function for peak grouping using mzClust |
| doubleMatrix | Allocate double, integer, or logical matricies |
| DratioFilter | Filter features based on the dispersion ratio |
| estimatePrecursorIntensity | Estimate precursor intensity for MS level 2 spectra |
| etg | Empirically Transformed Gaussian function |
| exportMetaboAnalyst | Export data for use in MetaboAnalyst |
| extractMsData-method | DEPRECATED: Extract a 'data.frame' containing MS data |
| featureChromatograms | Extract ion chromatograms for each feature |
| feature-grouping | Compounding of LC-MS features |
| featureSpectra | Extract spectra associated with features |
| featureSummary | Simple feature summaries |
| fillChromPeaks | Gap Filling |
| 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 |
| filterFeatures | Filtering of features based on conventional quality... |
| filter-MChromatograms | Filtering sets of chromatographic data |
| filtfft | Apply an convolution filter using an FFT |
| findChromPeaks | Chromatographic Peak Detection |
| findChromPeaks-centWave | Chromatographic peak detection using the centWave method |
| findChromPeaks-centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes |
| findChromPeaks-Chromatogram-CentWaveParam | centWave-based peak detection in purely chromatographic data |
| findChromPeaks-Chromatogram-MatchedFilter | matchedFilter-based peak detection in purely chromatographic... |
| findChromPeaksIsolationWindow | Data independent acquisition (DIA): peak detection in... |
| findChromPeaks-massifquant | Chromatographic peak detection using the massifquant method |
| findChromPeaks-matchedFilter | Peak detection in the chromatographic time domain |
| findEqualGreater | Find values in sorted vectors |
| findMZ | Find fragment ions in xcmsFragment objects |
| findneutral | Find neutral losses in xcmsFragment objects |
| findPeaks.addPredictedIsotopeFeatures-methods | Feature detection based on predicted isotope features for... |
| findPeaks.centWave-methods | Feature detection for high resolution LC/MS data |
| findPeaks.centWaveWithPredictedIsotopeROIs-methods | Feature detection with centWave and additional isotope... |
| findPeaks.massifquant-methods | Feature detection for XC-MS data. |
| findPeaks.matchedFilter-xcmsRaw-method | Peak 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 | Single-spectrum non-chromatography MS data peak detection |
| findPeaks.MSW-xcmsRaw-method | Peak detection for single-spectrum non-chromatography MS data |
| GenericParam | Generic parameter class |
| 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 |
| getXcmsRaw-methods | Load the raw data for one or more files in the xcmsSet |
| groupChromPeaks | Correspondence: group chromatographic peaks across samples |
| group.density | Group peaks from different samples together |
| groupFeatures-abundance-correlation | Compounding/feature grouping based on similarity of... |
| groupFeatures-eic-similarity | Compounding/feature grouping based on similarity of extracted... |
| groupFeatures-similar-rtime | Compounding/feature grouping based on similar retention times |
| group-methods | Group peaks from different samples together |
| group.mzClust | Group Peaks via High Resolution Alignment |
| groupnames-methods | Generate unque names for peak groups |
| groupnames-XCMSnExp | Generate unique group (feature) names based on mass and... |
| group.nearest | Group peaks from different samples together |
| groupOverlaps | Group overlapping ranges |
| groupval-methods | Extract a matrix of peak values for each group |
| highlightChromPeaks | Add definition of chromatographic peaks to an extracted... |
| image.xcmsRaw | Plot log intensity image of a xcmsRaw object |
| imputeLinInterpol | Impute values for empty elements in a vector using linear... |
| imputeRowMin | Replace missing values with a proportion of the row minimum |
| imputeRowMinRand | Impute missing values with random numbers based on the row... |
| isolationWindowTargetMz-OnDiskMSnExp-method | Extract isolation window target m/z definition |
| LamaParama | Landmark-based alignment: aligning a dataset against an... |
| levelplot.xcmsRaw | Plot log intensity image of a xcmsRaw object |
| loadRaw-methods | Read binary data from a source |
| loadXcmsData | LC-MS preprocessing result test data sets |
| manualChromPeaks | Manual peak integration and feature definition |
| 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 |
| overlappingFeatures | Identify overlapping features |
| panel.cor | Correlation coefficient panel for pairs function |
| peakPlots-methods | Plot a grid of a large number of peaks |
| peaksWithCentWave | Identify peaks in chromatographic data using centWave |
| peaksWithMatchedFilter | Identify peaks in chromatographic data using matchedFilter |
| peakTable-methods | Create report of aligned peak intensities |
| PercentMissingFilter | Filter features based on the percentage of missing data |
| phenoDataFromPaths | Derive experimental design from file paths |
| PlainTextParam | Store contents of 'MsExperiment' and 'XcmsExperiment' objects... |
| plotAdjustedRtime | Visualization of Alignment Results |
| plotChromatogramsOverlay | Plot multiple chromatograms into the same plot |
| plotChrom-methods | Plot extracted ion chromatograms from the profile matrix |
| plotChromPeakDensity | Plot chromatographic peak density along the retention time... |
| plotChromPeaks | General visualizations of peak detection results |
| plotEIC-methods | Plot extracted ion chromatograms for specified m/z range |
| plotFeatureGroups | Plot feature groups in the m/z-retention time space |
| plotMsData | DEPRECATED: Create a plot that combines a XIC and a mz/rt 2D... |
| plotPeaks-methods | Plot a grid of a large number of peaks |
| plotQC | Plot m/z and RT deviations for QC purposes without external... |
| 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 |
| ProcessHistory-class | Tracking data processing |
| profGenerate | Generation of profile data |
| profMat-xcmsSet | The profile matrix |
| 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 |
| rawEIC-methods | Get extracted ion chromatograms for specified m/z range |
| rawMat-methods | Get a raw data matrix |
| RDataParam | Store 'XcmsExperiment' object as .RData file |
| reconstructChromPeakSpectra | Data independent acquisition (DIA): reconstruct MS2 spectra |
| rectUnique | Determine a subset of rectangles with unique, non-overlapping... |
| refineChromPeaks | Refine Identified Chromatographic Peaks |
| removeIntensity-Chromatogram | Remove intensities from chromatographic data |
| 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 |
| rla | Calculate relative log abundances |
| RsdFilter | Filter features based on their coefficient of variation |
| sampnames-methods | Get sample names |
| showError-xcmsSet-method | Extract processing errors |
| 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 |
| storeResults | Save xcms result objects in a specified format |
| sub-xcmsRaw-logicalOrNumeric-missing-missing-method | Subset an xcmsRaw object by scans |
| updateObject-xcmsSet-method | Update an 'xcmsSet' object |
| useOriginalCode | Enable usage of old xcms code |
| verify.mzQuantML | Verify an mzQuantML file |
| write.cdf-methods | Save an xcmsRaw object to file |
| writeMSData-XCMSnExp-character-method | Export MS data to mzML/mzXML files |
| write.mzdata-methods | Save an xcmsRaw object to a file |
| write.mzQuantML | Save an xcmsSet object to an PSI mzQuantML file |
| writeMzTab | Save a grouped xcmsSet object in mzTab-1.1 format file |
| XChromatogram | Containers for chromatographic and peak detection data |
| xcms-deprecated | Deprecated functions in package 'xcms' |
| xcmsEIC-class | Class xcmsEIC, a class for multi-sample extracted ion... |
| XcmsExperiment | Next Generation 'xcms' Result Object |
| 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... |
| XCMSnExp-class | Data container storing xcms preprocessing results |
| XCMSnExp-filter-methods | XCMSnExp filtering and subsetting |
| XCMSnExp-inherited-methods | XCMSnExp data manipulation methods inherited from MSnbase |
| XCMSnExp-peak-grouping-results | Accessing mz-rt feature data values |
| 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 |
