A B C D E F G H I K L M N O P R S T U V W X misc
absent | Determine which peaks are absent / present in a sample class |
absent-method | Determine which peaks are absent / present in a sample class |
absMz | High resolution peak grouping for single spectra samples |
absMz-method | High resolution peak grouping for single spectra samples |
absMz-method | Peak grouping based on proximity in the mz-rt space |
absMz<- | High resolution peak grouping for single spectra samples |
absMz<--method | High resolution peak grouping for single spectra samples |
absMz<--method | Peak grouping based on proximity in the mz-rt space |
absRt | Peak grouping based on proximity in the mz-rt space |
absRt-method | Peak grouping based on proximity in the mz-rt space |
absRt<- | Peak grouping based on proximity in the mz-rt space |
absRt<--method | Peak grouping based on proximity in the mz-rt space |
addParams | Single-spectrum non-chromatography MS data peak detection |
addParams-method | Single-spectrum non-chromatography MS data peak detection |
addParams<- | Single-spectrum non-chromatography MS data peak detection |
addParams<--method | Single-spectrum non-chromatography MS data peak detection |
adjustedRtime | Data container storing xcms preprocessing results |
adjustedRtime-method | Data container storing xcms preprocessing results |
adjustedRtime<- | Data container storing xcms preprocessing results |
adjustedRtime<--method | Data container storing xcms preprocessing results |
adjustRtime | Alignment: Retention time correction methods. |
adjustRtime-method | Align retention times across samples using Obiwarp |
adjustRtime-method | Retention time correction based on alignment of house keeping peak groups |
adjustRtime-obiwarp | Align retention times across samples using Obiwarp |
adjustRtime-peakGroups | Retention time correction based on alignment of house keeping peak groups |
adjustRtimePeakGroups | Retention time correction based on alignment of house keeping peak groups |
ampTh | Single-spectrum non-chromatography MS data peak detection |
ampTh-method | Single-spectrum non-chromatography MS data peak detection |
ampTh<- | Single-spectrum non-chromatography MS data peak detection |
ampTh<--method | Single-spectrum non-chromatography MS data peak detection |
applyAdjustedRtime | Replace raw with adjusted retention times |
AutoLockMass | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
AutoLockMass-method | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
AutoLockMass-methods | Automatic parameter for Lock mass fixing 'AutoLockMass' ~~ |
baseValue | Peak detection in the chromatographic time domain |
baseValue-method | Peak detection in the chromatographic time domain |
baseValue<- | Peak detection in the chromatographic time domain |
baseValue<--method | Peak detection in the chromatographic time domain |
bin-method | XCMSnExp data manipulation methods inherited from MSnbase |
binSize | Peak detection in the chromatographic time domain |
binSize-method | Align retention times across samples using Obiwarp |
binSize-method | Peak detection in the chromatographic time domain |
binSize-method | Peak grouping based on time dimension peak densities |
binSize<- | Peak detection in the chromatographic time domain |
binSize<--method | Align retention times across samples using Obiwarp |
binSize<--method | Peak detection in the chromatographic time domain |
binSize<--method | Peak grouping based on time dimension peak densities |
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 |
bw | Peak grouping based on time dimension peak densities |
bw-method | Peak grouping based on time dimension peak densities |
bw<- | Peak grouping based on time dimension peak densities |
bw<--method | Peak grouping based on time dimension peak densities |
c, c-methods | Combine xcmsSet objects |
c.xcmsSet | Combine xcmsSet objects |
CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks |
CalibrantMassParam-class | Calibrant mass based calibration of chromatgraphic peaks |
calibrate | Calibrate peaks for correcting unprecise m/z values |
calibrate-method | Calibrant mass based calibration of chromatgraphic peaks |
calibrate-method | Calibrate peaks for correcting unprecise m/z values |
centerSample | Align retention times across samples using Obiwarp |
centerSample-method | Align retention times across samples using Obiwarp |
centerSample<- | Align retention times across samples using Obiwarp |
centerSample<--method | Align retention times across samples using Obiwarp |
centWave | Chromatographic peak detection using the centWave method |
CentWaveParam | Chromatographic peak detection using the centWave method |
CentWaveParam-class | Chromatographic peak detection using the centWave method |
CentWavePredIsoParam | Two-step centWave peak detection considering also isotopes |
CentWavePredIsoParam-class | Two-step centWave peak detection considering also isotopes |
centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes |
checkBack | Chromatographic peak detection using the massifquant method |
checkBack-method | Chromatographic peak detection using the massifquant method |
checkBack<- | Chromatographic peak detection using the massifquant method |
checkBack<--method | Chromatographic peak detection using the massifquant method |
chromatogram | Extracting chromatograms |
chromatogram-method | Extracting chromatograms |
chromatographic-peak-detection | Chromatographic peak detection methods. |
chromPeaks | Data container storing xcms preprocessing results |
chromPeaks-method | Data container storing xcms preprocessing results |
chromPeaks<- | Data container storing xcms preprocessing results |
chromPeaks<--method | Data container storing xcms preprocessing results |
clean-method | XCMSnExp data manipulation methods inherited from MSnbase |
collect | Collect MS^n peaks into xcmsFragments |
collect-method | Collect MS^n peaks into xcmsFragments |
collect-methods | Collect MS^n peaks into xcmsFragments |
consecMissedLimit | Chromatographic peak detection using the massifquant method |
consecMissedLimit-method | Chromatographic peak detection using the massifquant method |
consecMissedLimit<- | Chromatographic peak detection using the massifquant method |
consecMissedLimit<--method | Chromatographic peak detection using the massifquant method |
criticalValue | Chromatographic peak detection using the massifquant method |
criticalValue-method | Chromatographic peak detection using the massifquant method |
criticalValue<- | Chromatographic peak detection using the massifquant method |
criticalValue<--method | Chromatographic peak detection using the massifquant method |
deepCopy | Constructor for xcmsRaw objects which reads NetCDF/mzXML files |
deepCopy-method | Constructor for xcmsRaw objects which reads NetCDF/mzXML files |
diffreport | Create report of analyte differences |
diffreport-method | Create report of analyte differences |
distance | Peak detection in the chromatographic time domain |
distance-method | Peak detection in the chromatographic time domain |
distance<- | Peak detection in the chromatographic time domain |
distance<--method | Peak detection in the chromatographic time domain |
distFun | Align retention times across samples using Obiwarp |
distFun-method | Align retention times across samples using Obiwarp |
distFun<- | Align retention times across samples using Obiwarp |
distFun<--method | Align retention times across samples using Obiwarp |
do_adjustRtime_peakGroups | Align spectrum retention times across samples using peak groups found in most samples |
do_findChromPeaks_addPredIsoROIs | Core API function for two-step centWave peak detection with isotopes |
do_findChromPeaks_centWave | Core API function for centWave peak detection |
do_findChromPeaks_centWaveWithPredIsoROIs | Core API function for two-step centWave peak detection with isotopes |
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 data peak detection |
do_groupChromPeaks_density | Core API function for peak density based chromatographic peak grouping |
do_groupChromPeaks_nearest | Core API function for chromatic peak grouping using a nearest neighbor approach |
do_groupPeaks_mzClust | Core API function for peak grouping using mzClust |
dropAdjustedRtime | Data container storing xcms preprocessing results |
dropAdjustedRtime-method | Data container storing xcms preprocessing results |
dropChromPeaks | Data container storing xcms preprocessing results |
dropChromPeaks-method | Data container storing xcms preprocessing results |
dropFeatureDefinitions | Data container storing xcms preprocessing results |
dropFeatureDefinitions-method | Data container storing xcms preprocessing results |
dropFilledChromPeaks | Data container storing xcms preprocessing results |
dropFilledChromPeaks-method | Data container storing xcms preprocessing results |
etg | Empirically Transformed Gaussian function |
expandMz | Integrate areas of missing peaks |
expandMz-method | Integrate areas of missing peaks |
expandMz<- | Integrate areas of missing peaks |
expandMz<--method | Integrate areas of missing peaks |
expandRt | Integrate areas of missing peaks |
expandRt-method | Integrate areas of missing peaks |
expandRt<- | Integrate areas of missing peaks |
expandRt<--method | Integrate areas of missing peaks |
extractChromatograms | Deprecated functions in package 'xcms' |
extractChromatograms-method | Deprecated functions in package 'xcms' |
extractMsData | Extract a 'data.frame' containing MS data |
extractMsData-method | Extract a 'data.frame' containing MS data |
extraPeaks | Retention time correction based on alignment of house keeping peak groups |
extraPeaks-method | Retention time correction based on alignment of house keeping peak groups |
extraPeaks<- | Retention time correction based on alignment of house keeping peak groups |
extraPeaks<--method | Retention time correction based on alignment of house keeping peak groups |
factorDiag | Align retention times across samples using Obiwarp |
factorDiag-method | Align retention times across samples using Obiwarp |
factorDiag<- | Align retention times across samples using Obiwarp |
factorDiag<--method | Align retention times across samples using Obiwarp |
factorGap | Align retention times across samples using Obiwarp |
factorGap-method | Align retention times across samples using Obiwarp |
factorGap<- | Align retention times across samples using Obiwarp |
factorGap<--method | Align retention times across samples using Obiwarp |
family | Retention time correction based on alignment of house keeping peak groups |
family-method | Retention time correction based on alignment of house keeping peak groups |
family<- | Retention time correction based on alignment of house keeping peak groups |
family<--method | Retention time correction based on alignment of house keeping peak groups |
featureDefinitions | Data container storing xcms preprocessing results |
featureDefinitions-method | Data container storing xcms preprocessing results |
featureDefinitions<- | Data container storing xcms preprocessing results |
featureDefinitions<--method | Data container storing xcms preprocessing results |
featureValues | Accessing mz-rt feature data values |
featureValues-method | Accessing mz-rt feature data values |
fileIndex | Tracking data processing |
fileIndex-method | Tracking data processing |
filepaths | Class xcmsSet, a class for preprocessing peak data |
filepaths-method | Class xcmsSet, a class for preprocessing peak data |
filepaths<- | Class xcmsSet, a class for preprocessing peak data |
filepaths<--method | Class xcmsSet, a class for preprocessing peak data |
fillChromPeaks | Integrate areas of missing peaks |
fillChromPeaks-method | Integrate areas of missing peaks |
FillChromPeaksParam | Integrate areas of missing peaks |
FillChromPeaksParam-class | Integrate areas of missing peaks |
fillPeaks | Integrate areas of missing peaks |
fillPeaks-method | Integrate areas of missing peaks |
fillPeaks.chrom | Integrate areas of missing peaks |
fillPeaks.chrom-method | Integrate areas of missing peaks |
fillPeaks.MSW | Integrate areas of missing peaks in FTICR-MS data |
fillPeaks.MSW-method | Integrate areas of missing peaks in FTICR-MS data |
filterAcquisitionNum-method | XCMSnExp data manipulation methods inherited from MSnbase |
filterFile-method | XCMSnExp filtering and subsetting |
filterMsLevel-method | XCMSnExp filtering and subsetting |
filterMz-method | XCMSnExp filtering and subsetting |
filterRt-method | XCMSnExp filtering and subsetting |
findChromPeaks | Chromatographic peak detection methods. |
findChromPeaks-centWave | Chromatographic peak detection using the centWave method |
findChromPeaks-centWaveWithPredIsoROIs | Two-step centWave peak detection considering also isotopes |
findChromPeaks-massifquant | Chromatographic peak detection using the massifquant method |
findChromPeaks-matchedFilter | Peak detection in the chromatographic time domain |
findChromPeaks-method | Data container storing xcms preprocessing results |
findChromPeaks-method | Chromatographic peak detection using the centWave method |
findChromPeaks-method | Two-step centWave peak detection considering also isotopes |
findChromPeaks-method | Chromatographic peak detection using the massifquant method |
findChromPeaks-method | Peak detection in the chromatographic time domain |
findChromPeaks-method | Single-spectrum non-chromatography MS data peak detection |
findMZ | Find fragment ions in xcmsFragment objects |
findMZ-method | Find fragment ions in xcmsFragment objects |
findneutral | Find neutral losses in xcmsFragment objects |
findneutral-method | Find neutral losses in xcmsFragment objects |
findPeaks | Feature detection for GC/MS and LC/MS Data - methods |
findPeaks-method | Feature detection for GC/MS and LC/MS Data - methods |
findPeaks-methods | Feature detection for GC/MS and LC/MS Data - methods |
findPeaks-MSW | Single-spectrum non-chromatography MS data peak detection |
findPeaks.addPredictedIsotopeFeatures | Feature detection based on predicted isotope features for high resolution LC/MS data |
findPeaks.addPredictedIsotopeFeatures-method | Feature detection based on predicted isotope features for high resolution LC/MS data |
findPeaks.centWave | Feature detection for high resolution LC/MS data |
findPeaks.centWave-method | Feature detection for high resolution LC/MS data |
findPeaks.centWaveWithPredictedIsotopeROIs | Feature detection with centWave and additional isotope features |
findPeaks.centWaveWithPredictedIsotopeROIs-method | Feature detection with centWave and additional isotope features |
findPeaks.massifquant | Feature detection for XC-MS data. |
findPeaks.massifquant-method | Feature detection for XC-MS data. |
findPeaks.matchedFilter | Peak detection in the chromatographic time domain |
findPeaks.matchedFilter-method | Peak detection in the chromatographic time domain |
findPeaks.MS1 | Collecting MS1 precursor peaks |
findPeaks.MS1-method | Collecting MS1 precursor peaks |
findPeaks.MSW | Peak detection for single-spectrum non-chromatography MS data |
findPeaks.MSW-method | Peak detection for single-spectrum non-chromatography MS data |
firstBaselineCheck | Chromatographic peak detection using the centWave method |
firstBaselineCheck-method | Chromatographic peak detection using the centWave method |
firstBaselineCheck<- | Chromatographic peak detection using the centWave method |
firstBaselineCheck<--method | Chromatographic peak detection using the centWave method |
fitgauss | Chromatographic peak detection using the centWave method |
fitgauss-method | Chromatographic peak detection using the centWave method |
fitgauss-method | Chromatographic peak detection using the massifquant method |
fitgauss<- | Chromatographic peak detection using the centWave method |
fitgauss<--method | Chromatographic peak detection using the centWave method |
fitgauss<--method | Chromatographic peak detection using the massifquant method |
fwhm | Peak detection in the chromatographic time domain |
fwhm-method | Peak detection in the chromatographic time domain |
fwhm<- | Peak detection in the chromatographic time domain |
fwhm<--method | Peak detection in the chromatographic time domain |
gapExtend | Align retention times across samples using Obiwarp |
gapExtend-method | Align retention times across samples using Obiwarp |
gapExtend<- | Align retention times across samples using Obiwarp |
gapExtend<--method | Align retention times across samples using Obiwarp |
gapInit | Align retention times across samples using Obiwarp |
gapInit-method | Align retention times across samples using Obiwarp |
gapInit<- | Align retention times across samples using Obiwarp |
gapInit<--method | Align retention times across samples using Obiwarp |
GenericParam | Generic parameter class |
GenericParam-class | Generic parameter class |
getEIC | Get extracted ion chromatograms for specified m/z ranges |
getEIC-method | Get extracted ion chromatograms for specified m/z ranges |
getMsnScan | Get m/z and intensity values for a single mass scan |
getMsnScan-method | Get m/z and intensity values for a single mass scan |
getPeaks | Get peak intensities for specified regions |
getPeaks-method | Get peak intensities for specified regions |
getScan | Get m/z and intensity values for a single mass scan |
getScan-method | Get m/z and intensity values for a single mass scan |
getSpec | Get average m/z and intensity values for multiple mass scans |
getSpec-method | Get average m/z and intensity values for multiple mass scans |
getXcmsRaw | Load the raw data for one or more files in the xcmsSet |
getXcmsRaw-method | Load the raw data for one or more files in the xcmsSet |
group | Group peaks from different samples together |
group-method | Group peaks from different samples together |
group-methods | Group peaks from different samples together |
group.density | Group peaks from different samples together |
group.density-method | Group peaks from different samples together |
group.mzClust | Group Peaks via High Resolution Alignment |
group.mzClust-method | Group Peaks via High Resolution Alignment |
group.nearest | Group peaks from different samples together |
group.nearest-method | Group peaks from different samples together |
groupChromPeaks | Correspondence: Chromatographic peak grouping methods. |
groupChromPeaks-density | Peak grouping based on time dimension peak densities |
groupChromPeaks-method | Peak grouping based on time dimension peak densities |
groupChromPeaks-method | High resolution peak grouping for single spectra samples |
groupChromPeaks-method | Peak grouping based on proximity in the mz-rt space |
groupChromPeaks-mzClust | High resolution peak grouping for single spectra samples |
groupChromPeaks-nearest | Peak grouping based on proximity in the mz-rt space |
groupidx | Class xcmsSet, a class for preprocessing peak data |
groupidx-method | Class xcmsSet, a class for preprocessing peak data |
groupidx<- | Class xcmsSet, a class for preprocessing peak data |
groupidx<--method | Class xcmsSet, a class for preprocessing peak data |
groupnames | Generate unque names for peak groups |
groupnames-method | Generate unque names for peak groups |
groups | Class xcmsSet, a class for preprocessing peak data |
groups-method | Class xcmsSet, a class for preprocessing peak data |
groups<- | Class xcmsSet, a class for preprocessing peak data |
groups<--method | Class xcmsSet, a class for preprocessing peak data |
groupval | Extract a matrix of peak values for each group |
groupval-method | Extract a matrix of peak values for each group |
hasAdjustedRtime | Data container storing xcms preprocessing results |
hasAdjustedRtime-method | Data container storing xcms preprocessing results |
hasChromPeaks | Data container storing xcms preprocessing results |
hasChromPeaks-method | Data container storing xcms preprocessing results |
hasFeatures | Data container storing xcms preprocessing results |
hasFeatures-method | Data container storing xcms preprocessing results |
highlightChromPeaks | Add definition of chromatographic peaks to an extracted chromatogram plot |
image-method | Plot log intensity image of a xcmsRaw object |
impute-method | Peak detection in the chromatographic time domain |
impute<- | Peak detection in the chromatographic time domain |
impute<--method | Peak detection in the chromatographic time domain |
imputeLinInterpol | Impute values for empty elements in a vector using linear interpolation |
index | Peak detection in the chromatographic time domain |
index-method | Peak detection in the chromatographic time domain |
index<- | Peak detection in the chromatographic time domain |
index<--method | Peak detection in the chromatographic time domain |
initPenalty | Align retention times across samples using Obiwarp |
initPenalty-method | Align retention times across samples using Obiwarp |
initPenalty<- | Align retention times across samples using Obiwarp |
initPenalty<--method | Align retention times across samples using Obiwarp |
integrate-method | Chromatographic peak detection using the centWave method |
integrate-method | Chromatographic peak detection using the massifquant method |
integrate<- | Chromatographic peak detection using the centWave method |
integrate<--method | Chromatographic peak detection using the centWave method |
integrate<--method | Chromatographic peak detection using the massifquant method |
intensity-method | Data container storing xcms preprocessing results |
isCalibrated | Calibrant mass based calibration of chromatgraphic peaks |
kNN | Peak grouping based on proximity in the mz-rt space |
kNN-method | Peak grouping based on proximity in the mz-rt space |
kNN<- | Peak grouping based on proximity in the mz-rt space |
kNN<--method | Peak grouping based on proximity in the mz-rt space |
levelplot | Class xcmsRaw, a class for handling raw data |
levelplot-method | Plot log intensity image of a xcmsRaw object |
loadRaw | Read binary data from a source |
loadRaw-method | Read binary data from a source |
loadRaw-methods | Read binary data from a source |
localAlignment | Align retention times across samples using Obiwarp |
localAlignment-method | Align retention times across samples using Obiwarp |
localAlignment<- | Align retention times across samples using Obiwarp |
localAlignment<--method | Align retention times across samples using Obiwarp |
makeacqNum | Correct gaps in data |
makeacqNum-method | Correct gaps in data |
massifquant | Chromatographic peak detection using the massifquant method |
MassifquantParam | Chromatographic peak detection using the massifquant method |
MassifquantParam-class | Chromatographic peak detection using the massifquant method |
matchedFilter | Peak detection in the chromatographic time domain |
MatchedFilterParam | Peak detection in the chromatographic time domain |
MatchedFilterParam-class | Peak detection in the chromatographic time domain |
max-method | Peak detection in the chromatographic time domain |
max<- | Peak detection in the chromatographic time domain |
max<--method | Peak detection in the chromatographic time domain |
maxCharge | Two-step centWave peak detection considering also isotopes |
maxCharge-method | Two-step centWave peak detection considering also isotopes |
maxCharge<- | Two-step centWave peak detection considering also isotopes |
maxCharge<--method | Two-step centWave peak detection considering also isotopes |
maxFeatures | Peak grouping based on time dimension peak densities |
maxFeatures-method | Peak grouping based on time dimension peak densities |
maxFeatures<- | Peak grouping based on time dimension peak densities |
maxFeatures<--method | Peak grouping based on time dimension peak densities |
maxIso | Two-step centWave peak detection considering also isotopes |
maxIso-method | Two-step centWave peak detection considering also isotopes |
maxIso<- | Two-step centWave peak detection considering also isotopes |
maxIso<--method | Two-step centWave peak detection considering also isotopes |
medianFilter | Apply a median filter to a matrix |
minFraction | Peak grouping based on time dimension peak densities |
minFraction-method | Retention time correction based on alignment of house keeping peak groups |
minFraction-method | Peak grouping based on time dimension peak densities |
minFraction-method | High resolution peak grouping for single spectra samples |
minFraction<- | Peak grouping based on time dimension peak densities |
minFraction<--method | Retention time correction based on alignment of house keeping peak groups |
minFraction<--method | Peak grouping based on time dimension peak densities |
minFraction<--method | High resolution peak grouping for single spectra samples |
minNoiseLevel | Single-spectrum non-chromatography MS data peak detection |
minNoiseLevel-method | Single-spectrum non-chromatography MS data peak detection |
minNoiseLevel<- | Single-spectrum non-chromatography MS data peak detection |
minNoiseLevel<--method | Single-spectrum non-chromatography MS data peak detection |
minSamples | Peak grouping based on time dimension peak densities |
minSamples-method | Peak grouping based on time dimension peak densities |
minSamples-method | High resolution peak grouping for single spectra samples |
minSamples<- | Peak grouping based on time dimension peak densities |
minSamples<--method | Peak grouping based on time dimension peak densities |
minSamples<--method | High resolution peak grouping for single spectra samples |
mslevel | Class xcmsSet, a class for preprocessing peak data |
msLevel-method | Tracking data processing |
mslevel-method | Class xcmsRaw, a class for handling raw data |
mslevel-method | Class xcmsSet, a class for preprocessing peak data |
msn2xcmsRaw | Copy MSn data in an xcmsRaw to the MS slots |
MSW | Single-spectrum non-chromatography MS data peak detection |
MSWParam | Single-spectrum non-chromatography MS data peak detection |
MSWParam-class | Single-spectrum non-chromatography MS data peak detection |
mz,CalibrantMassParam | Calibrant mass based calibration of chromatgraphic peaks |
mz-method | Data container storing xcms preprocessing results |
mzCenterFun | Chromatographic peak detection using the centWave method |
mzCenterFun-method | Chromatographic peak detection using the centWave method |
mzCenterFun-method | Chromatographic peak detection using the massifquant method |
mzCenterFun<- | Chromatographic peak detection using the centWave method |
mzCenterFun<--method | Chromatographic peak detection using the centWave method |
mzCenterFun<--method | Chromatographic peak detection using the massifquant method |
MzClustParam | High resolution peak grouping for single spectra samples |
MzClustParam-class | High resolution peak grouping for single spectra samples |
mzdiff | Chromatographic peak detection using the centWave method |
mzdiff-method | Chromatographic peak detection using the centWave method |
mzdiff-method | Chromatographic peak detection using the massifquant method |
mzdiff-method | Peak detection in the chromatographic time domain |
mzdiff<- | Chromatographic peak detection using the centWave method |
mzdiff<--method | Chromatographic peak detection using the centWave method |
mzdiff<--method | Chromatographic peak detection using the massifquant method |
mzdiff<--method | Peak detection in the chromatographic time domain |
mzIntervalExtension | Two-step centWave peak detection considering also isotopes |
mzIntervalExtension-method | Two-step centWave peak detection considering also isotopes |
mzIntervalExtension<- | Two-step centWave peak detection considering also isotopes |
mzIntervalExtension<--method | Two-step centWave peak detection considering also isotopes |
mzrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
mzrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
mzVsRtBalance | Peak grouping based on proximity in the mz-rt space |
mzVsRtBalance-method | Peak grouping based on proximity in the mz-rt space |
mzVsRtBalance<- | Peak grouping based on proximity in the mz-rt space |
mzVsRtBalance<--method | Peak grouping based on proximity in the mz-rt space |
nearbyPeak | Single-spectrum non-chromatography MS data peak detection |
nearbyPeak-method | Single-spectrum non-chromatography MS data peak detection |
nearbyPeak<- | Single-spectrum non-chromatography MS data peak detection |
nearbyPeak<--method | Single-spectrum non-chromatography MS data peak detection |
NearestPeaksParam | Peak grouping based on proximity in the mz-rt space |
NearestPeaksParam-class | Peak grouping based on proximity in the mz-rt space |
noise | Chromatographic peak detection using the centWave method |
noise-method | Chromatographic peak detection using the centWave method |
noise-method | Chromatographic peak detection using the massifquant method |
noise<- | Chromatographic peak detection using the centWave method |
noise<--method | Chromatographic peak detection using the centWave method |
noise<--method | Chromatographic peak detection using the massifquant method |
normalize-method | XCMSnExp data manipulation methods inherited from MSnbase |
ObiwarpParam | Align retention times across samples using Obiwarp |
ObiwarpParam-class | Align retention times across samples using Obiwarp |
PeakDensityParam | Peak grouping based on time dimension peak densities |
PeakDensityParam-class | Peak grouping based on time dimension peak densities |
peakGroupsMatrix | Retention time correction based on alignment of house keeping peak groups |
peakGroupsMatrix-method | Retention time correction based on alignment of house keeping peak groups |
peakGroupsMatrix<- | Retention time correction based on alignment of house keeping peak groups |
peakGroupsMatrix<--method | Retention time correction based on alignment of house keeping peak groups |
PeakGroupsParam | Retention time correction based on alignment of house keeping peak groups |
PeakGroupsParam-class | Retention time correction based on alignment of house keeping peak groups |
peakPlots-method | Plot a grid of a large number of peaks |
peakPlots-methods | Plot a grid of a large number of peaks |
peaks | Class xcmsSet, a class for preprocessing peak data |
peaks-method | Class xcmsSet, a class for preprocessing peak data |
peaks<- | Class xcmsSet, a class for preprocessing peak data |
peaks<--method | Class xcmsSet, a class for preprocessing peak data |
peakScaleRange | Single-spectrum non-chromatography MS data peak detection |
peakScaleRange-method | Single-spectrum non-chromatography MS data peak detection |
peakScaleRange<- | Single-spectrum non-chromatography MS data peak detection |
peakScaleRange<--method | Single-spectrum non-chromatography MS data peak detection |
peakTable | Create report of aligned peak intensities |
peakTable-method | Create report of aligned peak intensities |
peakThr | Single-spectrum non-chromatography MS data peak detection |
peakThr-method | Single-spectrum non-chromatography MS data peak detection |
peakThr<- | Single-spectrum non-chromatography MS data peak detection |
peakThr<--method | Single-spectrum non-chromatography MS data peak detection |
peakwidth | Chromatographic peak detection using the centWave method |
peakwidth-method | Chromatographic peak detection using the centWave method |
peakwidth-method | Chromatographic peak detection using the massifquant method |
peakwidth<- | Chromatographic peak detection using the centWave method |
peakwidth<--method | Chromatographic peak detection using the centWave method |
peakwidth<--method | Chromatographic peak detection using the massifquant method |
phenoData | Class xcmsSet, a class for preprocessing peak data |
phenoData-method | Class xcmsSet, a class for preprocessing peak data |
phenoData<- | Class xcmsSet, a class for preprocessing peak data |
phenoData<--method | Class xcmsSet, a class for preprocessing peak data |
phenoDataFromPaths | Derive experimental design from file paths |
pickPeaks-method | XCMSnExp data manipulation methods inherited from MSnbase |
plot, plot-methods | Plot extracted ion chromatograms from multiple files |
plot.xcmsEIC | Plot extracted ion chromatograms from multiple files |
plotAdjustedRtime | Visualization of alignment results |
plotChrom | Plot extracted ion chromatograms from the profile matrix |
plotChrom-method | Plot extracted ion chromatograms from the profile matrix |
plotChromatogram | Deprecated functions in package 'xcms' |
plotChromPeakDensity | Plot chromatographic peak density along the retention time axis |
plotChromPeakImage | General visualizations of peak detection results |
plotChromPeaks | General visualizations of peak detection results |
plotEIC | Plot extracted ion chromatograms for specified m/z range |
plotEIC-method | Plot extracted ion chromatograms for specified m/z range |
plotMsData | Create a plot that combines a XIC and a mz/rt 2D plot for one sample |
plotPeaks | Plot a grid of a large number of peaks |
plotPeaks-method | Plot a grid of a large number of peaks |
plotQC | Plot m/z and RT deviations for QC purposes without external reference data |
plotRaw | Scatterplot of raw data points |
plotRaw-method | Scatterplot of raw data points |
plotrt | Plot retention time deviation profiles |
plotrt-method | Plot retention time deviation profiles |
plotScan | Plot a single mass scan |
plotScan-method | Plot a single mass scan |
plotSpec | Plot mass spectra from the profile matrix |
plotSpec-method | Plot mass spectra from the profile matrix |
plotSurf | Plot profile matrix 3D surface using OpenGL |
plotSurf-method | Plot profile matrix 3D surface using OpenGL |
plotTIC | Plot total ion count |
plotTIC-method | Plot total ion count |
plotTree | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
plotTree-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
polarity-method | Two-step centWave peak detection considering also isotopes |
polarity<- | Two-step centWave peak detection considering also isotopes |
polarity<--method | Two-step centWave peak detection considering also isotopes |
ppm | Chromatographic peak detection using the centWave method |
ppm-method | Integrate areas of missing peaks |
ppm-method | Chromatographic peak detection using the centWave method |
ppm-method | Chromatographic peak detection using the massifquant method |
ppm-method | High resolution peak grouping for single spectra samples |
ppm<- | Chromatographic peak detection using the centWave method |
ppm<--method | Integrate areas of missing peaks |
ppm<--method | Chromatographic peak detection using the centWave method |
ppm<--method | Chromatographic peak detection using the massifquant method |
ppm<--method | High resolution peak grouping for single spectra samples |
prefilter | Chromatographic peak detection using the centWave method |
prefilter-method | Chromatographic peak detection using the centWave method |
prefilter-method | Chromatographic peak detection using the massifquant method |
prefilter<- | Chromatographic peak detection using the centWave method |
prefilter<--method | Chromatographic peak detection using the centWave method |
prefilter<--method | Chromatographic peak detection using the massifquant method |
present | Determine which peaks are absent / present in a sample class |
present-method | Determine which peaks are absent / present in a sample class |
processDate | Tracking data processing |
processDate-method | Tracking data processing |
ProcessHistory | Tracking data processing |
processHistory | Data container storing xcms preprocessing results |
ProcessHistory-class | Tracking data processing |
processHistory-method | Data container storing xcms preprocessing results |
processHistoryTypes | Data container storing xcms preprocessing results |
processInfo | Tracking data processing |
processInfo-method | Tracking data processing |
processParam | Tracking data processing |
processParam-method | Tracking data processing |
processType | Tracking data processing |
processType-method | Tracking data processing |
profile-matrix | The profile matrix |
profinfo | Class xcmsSet, a class for preprocessing peak data |
profinfo-method | Class xcmsRaw, a class for handling raw data |
profinfo-method | Class xcmsSet, a class for preprocessing peak data |
profinfo<- | Class xcmsSet, a class for preprocessing peak data |
profinfo<--method | Class xcmsSet, a class for preprocessing peak data |
profMat | The profile matrix |
profMat-method | Data container storing xcms preprocessing results |
profMat-method | The profile matrix |
profMat-xcmsSet | The profile matrix |
profMedFilt | Median filtering of the profile matrix |
profMedFilt-method | Median filtering of the profile matrix |
profMethod | Get and set method for generating profile data |
profMethod-method | Get and set method for generating profile data |
profMethod-method | Class xcmsSet, a class for preprocessing peak data |
profMethod<- | Get and set method for generating profile data |
profMethod<--method | Get and set method for generating profile data |
profMz | Class xcmsRaw, a class for handling raw data |
profMz-method | Class xcmsRaw, a class for handling raw data |
profRange | Specify a subset of profile mode data |
profRange-method | Specify a subset of profile mode data |
profStep | Get and set m/z step for generating profile data |
profStep-method | Get and set m/z step for generating profile data |
profStep-method | Class xcmsSet, a class for preprocessing peak data |
profStep<- | Get and set m/z step for generating profile data |
profStep<--method | Get and set m/z step for generating profile data |
progressCallback | Class xcmsSet, a class for preprocessing peak data |
progressCallback-method | Class xcmsSet, a class for preprocessing peak data |
progressCallback<- | Class xcmsSet, a class for preprocessing peak data |
progressCallback<--method | Class xcmsSet, a class for preprocessing peak data |
rawEIC | Get extracted ion chromatograms for specified m/z range |
rawEIC-method | Get extracted ion chromatograms for specified m/z range |
rawMat | Get a raw data matrix |
rawMat-method | Get a raw data matrix |
rawMat-methods | Get a raw data matrix |
removePeaks-method | XCMSnExp data manipulation methods inherited from MSnbase |
response | Align retention times across samples using Obiwarp |
response-method | Align retention times across samples using Obiwarp |
response<- | Align retention times across samples using Obiwarp |
response<--method | Align retention times across samples using Obiwarp |
retcor | Correct retention time from different samples |
retcor-method | Correct retention time from different samples |
retcor-methods | Correct retention time from different samples |
retcor.linear | Align retention times across samples |
retcor.linear-method | Align retention times across samples |
retcor.loess | Align retention times across samples |
retcor.loess-method | Align retention times across samples |
retcor.obiwarp | Align retention times across samples with Obiwarp |
retcor.obiwarp-method | Align retention times across samples with Obiwarp |
retcor.peakgroups | Align retention times across samples |
retcor.peakgroups-method | Align retention times across samples |
retexp | Set retention time window to a specified width |
revMz | Class xcmsRaw, a class for handling raw data |
revMz-method | Class xcmsRaw, a class for handling raw data |
ridgeLength | Single-spectrum non-chromatography MS data peak detection |
ridgeLength-method | Single-spectrum non-chromatography MS data peak detection |
ridgeLength<- | Single-spectrum non-chromatography MS data peak detection |
ridgeLength<--method | Single-spectrum non-chromatography MS data peak detection |
roiList | Chromatographic peak detection using the centWave method |
roiList-method | Chromatographic peak detection using the centWave method |
roiList<- | Chromatographic peak detection using the centWave method |
roiList<--method | Chromatographic peak detection using the centWave method |
roiScales | Chromatographic peak detection using the centWave method |
roiScales-method | Chromatographic peak detection using the centWave method |
roiScales<- | Chromatographic peak detection using the centWave method |
roiScales<--method | Chromatographic peak detection using the centWave method |
rtime-method | Data container storing xcms preprocessing results |
rtrange | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
rtrange-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
sampclass | Class xcmsSet, a class for preprocessing peak data |
sampclass-method | Class xcmsSet, a class for preprocessing peak data |
sampclass<- | Class xcmsSet, a class for preprocessing peak data |
sampclass<--method | Class xcmsSet, a class for preprocessing peak data |
sampleGroups | Peak grouping based on time dimension peak densities |
sampleGroups-method | Peak grouping based on time dimension peak densities |
sampleGroups-method | High resolution peak grouping for single spectra samples |
sampleGroups-method | Peak grouping based on proximity in the mz-rt space |
sampleGroups<- | Peak grouping based on time dimension peak densities |
sampleGroups<--method | Peak grouping based on time dimension peak densities |
sampleGroups<--method | High resolution peak grouping for single spectra samples |
sampleGroups<--method | Peak grouping based on proximity in the mz-rt space |
sampnames | Get sample names |
sampnames-method | Get sample names |
sampnames<- | Class xcmsSet, a class for preprocessing peak data |
sampnames<--method | Class xcmsSet, a class for preprocessing peak data |
scales | Single-spectrum non-chromatography MS data peak detection |
scales-method | Single-spectrum non-chromatography MS data peak detection |
scales<- | Single-spectrum non-chromatography MS data peak detection |
scales<--method | Single-spectrum non-chromatography MS data peak detection |
scanrange | Class xcmsSet, a class for preprocessing peak data |
scanrange-method | Class xcmsRaw, a class for handling raw data |
scanrange-method | Class xcmsSet, a class for preprocessing peak data |
setAs | Data container storing xcms preprocessing results |
show-method | Generic parameter class |
show-method | Tracking data processing |
show-method | Data container storing xcms preprocessing results |
show-method | Align retention times across samples using Obiwarp |
show-method | Retention time correction based on alignment of house keeping peak groups |
show-method | Integrate areas of missing peaks |
show-method | Chromatographic peak detection using the centWave method |
show-method | Two-step centWave peak detection considering also isotopes |
show-method | Chromatographic peak detection using the massifquant method |
show-method | Peak detection in the chromatographic time domain |
show-method | Single-spectrum non-chromatography MS data peak detection |
show-method | Peak grouping based on time dimension peak densities |
show-method | High resolution peak grouping for single spectra samples |
show-method | Peak grouping based on proximity in the mz-rt space |
show-method | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
show-method | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
show-method | A matrix of peaks |
show-method | Class xcmsRaw, a class for handling raw data |
show-method | Class xcmsSet, a class for preprocessing peak data |
showError | Extract processing errors |
showError-method | Extract processing errors |
sigma | Peak detection in the chromatographic time domain |
sigma-method | Peak detection in the chromatographic time domain |
sigma<- | Peak detection in the chromatographic time domain |
sigma<--method | Peak detection in the chromatographic time domain |
smooth | Retention time correction based on alignment of house keeping peak groups |
smooth-method | XCMSnExp data manipulation methods inherited from MSnbase |
smooth-method | Retention time correction based on alignment of house keeping peak groups |
smooth<- | Retention time correction based on alignment of house keeping peak groups |
smooth<--method | Retention time correction based on alignment of house keeping peak groups |
snthresh | Chromatographic peak detection using the centWave method |
snthresh-method | Chromatographic peak detection using the centWave method |
snthresh-method | Chromatographic peak detection using the massifquant method |
snthresh-method | Peak detection in the chromatographic time domain |
snthresh-method | Single-spectrum non-chromatography MS data peak detection |
snthresh<- | Chromatographic peak detection using the centWave method |
snthresh<--method | Chromatographic peak detection using the centWave method |
snthresh<--method | Chromatographic peak detection using the massifquant method |
snthresh<--method | Peak detection in the chromatographic time domain |
snthresh<--method | Single-spectrum non-chromatography MS data peak detection |
snthreshIsoROIs | Two-step centWave peak detection considering also isotopes |
snthreshIsoROIs-method | Two-step centWave peak detection considering also isotopes |
snthreshIsoROIs<- | Two-step centWave peak detection considering also isotopes |
snthreshIsoROIs<--method | Two-step centWave peak detection considering also isotopes |
sortMz | Class xcmsRaw, a class for handling raw data |
sortMz-method | Class xcmsRaw, a class for handling raw data |
span | Retention time correction based on alignment of house keeping peak groups |
span-method | Retention time correction based on alignment of house keeping peak groups |
span<- | Retention time correction based on alignment of house keeping peak groups |
span<--method | Retention time correction based on alignment of house keeping peak groups |
specDist | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
specDist-method | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
specDist-methods | Distance methods for xcmsSet, xcmsRaw and xsAnnotate |
specDist.cosine | a Distance function based on matching peaks |
specDist.cosine-method | a Distance function based on matching peaks |
specDist.meanMZmatch | a Distance function based on matching peaks |
specDist.meanMZmatch-method | a Distance function based on matching peaks |
specDist.peakCount | a Distance function based on matching peaks |
specDist.peakCount-method | a Distance function based on matching peaks |
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 |
spectra-method | Data container storing xcms preprocessing results |
spectrapply-method | Data container storing xcms preprocessing results |
split, split-methods | Divide an xcmsSet object |
split-method | XCMSnExp filtering and subsetting |
split.xcmsRaw | Divide an xcmsRaw object |
split.xcmsSet | Divide an xcmsSet object |
SSgauss | Gaussian Model |
steps | Peak detection in the chromatographic time domain |
steps-method | Peak detection in the chromatographic time domain |
steps<- | Peak detection in the chromatographic time domain |
steps<--method | Peak detection in the chromatographic time domain |
stitch | Correct gaps in data |
stitch-method | Correct gaps in data |
stitch-methods | Correct gaps in data |
stitch.netCDF | Correct gaps in data |
stitch.xml | Correct gaps in data |
subset-xcmsRaw | Subset an xcmsRaw object by scans |
tuneIn | Single-spectrum non-chromatography MS data peak detection |
tuneIn-method | Single-spectrum non-chromatography MS data peak detection |
tuneIn<- | Single-spectrum non-chromatography MS data peak detection |
tuneIn<--method | Single-spectrum non-chromatography MS data peak detection |
unions | Chromatographic peak detection using the massifquant method |
unions-method | Chromatographic peak detection using the massifquant method |
unions<- | Chromatographic peak detection using the massifquant method |
unions<--method | Chromatographic peak detection using the massifquant method |
updateObject-method | Update an 'xcmsSet' object |
useOriginalCode | Enable usage of old xcms code |
verboseColumns | Chromatographic peak detection using the centWave method |
verboseColumns-method | Chromatographic peak detection using the centWave method |
verboseColumns-method | Chromatographic peak detection using the massifquant method |
verboseColumns-method | Single-spectrum non-chromatography MS data peak detection |
verboseColumns<- | Chromatographic peak detection using the centWave method |
verboseColumns<--method | Chromatographic peak detection using the centWave method |
verboseColumns<--method | Chromatographic peak detection using the massifquant method |
verboseColumns<--method | Single-spectrum non-chromatography MS data peak detection |
verify.mzQuantML | Verify an mzQuantML file |
withWave | Chromatographic peak detection using the massifquant method |
withWave-method | Chromatographic peak detection using the massifquant method |
withWave<- | Chromatographic peak detection using the massifquant method |
withWave<--method | Chromatographic peak detection using the massifquant method |
write.cdf | Save an xcmsRaw object to file |
write.cdf-method | Save an xcmsRaw object to file |
write.mzdata | Save an xcmsRaw object to a file |
write.mzdata-method | Save an xcmsRaw object to a file |
write.mzQuantML | Save an xcmsSet object to an PSI mzQuantML file |
write.mzQuantML-method | Save an xcmsSet object to an PSI mzQuantML file |
writeMzTab | Save a grouped xcmsSet object in mzTab-1.1 format file |
xcms-deprecated | Deprecated functions in package 'xcms' |
xcmsEIC-class | Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
xcmsFileSource-class | Base class for loading raw data from a file |
xcmsFragments | Constructor for xcmsFragments objects which holds Tandem MS peaks |
xcmsFragments-class | Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
XCMSnExp | Data container storing xcms preprocessing results |
XCMSnExp-class | Data container storing xcms preprocessing results |
XCMSnExp-filter | XCMSnExp filtering and subsetting |
xcmsPapply | _Deprecated_: xcmsPapply |
xcmsPeaks-class | A matrix of peaks |
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 |
xcmsSource | Create an 'xcmsSource' object in a flexible way |
xcmsSource-class | Virtual class for raw data sources |
xcmsSource-method | Base class for loading raw data from a file |
xcmsSource-method | Create an 'xcmsSource' object in a flexible way |
xcmsSource-methods | Create an 'xcmsSource' object in a flexible way |
XProcessHistory | Tracking data processing |
XProcessHistory-class | Tracking data processing |
$-method | Class xcmsSet, a class for preprocessing peak data |
$<--method | Class xcmsSet, a class for preprocessing peak data |
[-method | XCMSnExp filtering and subsetting |
[-method | Subset an xcmsRaw object by scans |
[-method | Class xcmsSet, a class for preprocessing peak data |
[[-method | XCMSnExp filtering and subsetting |