absent-methods | Determine which peaks are absent / present in a sample class |
adjustRtime | Alignment: Retention time correction methods. |
adjustRtime-obiwarp | Align retention times across samples using Obiwarp |
adjustRtime-peakGroups | Retention time correction based on alignment of house keeping... |
align-Chromatogram | Aligning chromatographic data |
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 |
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 |
chromatographic-peak-detection | Chromatographic peak detection methods. |
chromPeakSpectra | Extract (MS2) 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 |
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 |
featureSpectra | Extract (MS2) spectra associated with features |
featureSummary | Simple feature summaries |
fillChromPeaks | Integrate areas of missing peaks |
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 |
filter-MChromatograms | Filtering sets of chromatographic data |
filtfft | Apply an convolution filter using an FFT |
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: Chromatographic peak grouping methods. |
groupChromPeaks-density | Peak grouping based on time dimension peak densities |
groupChromPeaks-mzClust | High resolution peak grouping for single spectra samples |
groupChromPeaks-nearest | Peak grouping based on proximity in the mz-rt space |
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 |
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 |
levelplot.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 |
normalize-Chromatogram | Normalize chromatographic data |
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 |
phenoDataFromPaths | Derive experimental design from file paths |
plotAdjustedRtime | Visualization of alignment results |
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 |
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 |
reconstructChromPeakSpectra | Data independent acquisition (DIA): reconstruct MS2 spectra |
rectUnique | Determine a subset of rectangles with unique, non-overlapping... |
refineChromPeaks-clean | Remove chromatographic peaks with too large rt width |
refineChromPeaks-filter-intensity | Remove chromatographic peaks based on intensity |
refineChromPeaks-merge | Merge neighboring and overlapping 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 'rla' calculates the... |
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 |
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... |
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 |
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