filepaths |
Class xcmsSet, a class for preprocessing peak data |
filepaths,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
filepaths<- |
Class xcmsSet, a class for preprocessing peak data |
filepaths<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
fillPeaks |
Integrate areas of missing peaks |
fillPeaks,xcmsSet-method |
Integrate areas of missing peaks |
fillPeaks.chrom |
Integrate areas of missing peaks |
fillPeaks.chrom,xcmsSet-method |
Integrate areas of missing peaks |
fillPeaks.MSW |
Integrate areas of missing peaks in FTICR-MS data |
fillPeaks.MSW,xcmsSet-method |
Integrate areas of missing peaks in FTICR-MS data |
findPeaks |
Feature detection for GC/MS and LC/MS Data - methods |
findPeaks,xcmsRaw-method |
Feature detection for GC/MS and LC/MS Data - methods |
findPeaks-methods |
Feature detection for GC/MS and LC/MS Data - methods |
findPeaks.centWave |
Feature detection for high resolution LC/MS data |
findPeaks.centWave,xcmsRaw-method |
Feature detection for high resolution LC/MS data |
findPeaks.matchedFilter |
Feature detection in the chromatographic time domain |
findPeaks.matchedFilter,xcmsRaw-method |
Feature detection in the chromatographic time domain |
findPeaks.MS1 |
Collecting MS1 precursor peaks |
findPeaks.MS1,xcmsRaw-method |
Collecting MS1 precursor peaks |
findPeaks.MSW |
Feature detection for single-spectrum non-chromatography MS data |
findPeaks.MSW,xcmsRaw-method |
Feature detection for single-spectrum non-chromatography MS data |
getEIC |
Get extracted ion chromatograms for specified m/z ranges |
getEIC,xcmsRaw-method |
Get extracted ion chromatograms for specified m/z ranges |
getEIC,xcmsSet-method |
Get extracted ion chromatograms for specified m/z ranges |
getPeaks |
Get peak intensities for specified regions |
getPeaks,xcmsRaw-method |
Get peak intensities for specified regions |
getScan |
Get m/z and intensity values for a single mass scan |
getScan,xcmsRaw-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,xcmsRaw-method |
Get average m/z and intensity values for multiple mass scans |
group |
Group peaks from different samples together |
group,xcmsSet-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,xcmsSet-method |
Group peaks from different samples together |
group.mzClust |
Group Peaks via High Resolution Alignment |
group.mzClust,xcmsSet-method |
Group Peaks via High Resolution Alignment |
group.nearest |
Group peaks from different samples together |
group.nearest,xcmsSet-method |
Group peaks from different samples together |
groupidx |
Class xcmsSet, a class for preprocessing peak data |
groupidx,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
groupidx<- |
Class xcmsSet, a class for preprocessing peak data |
groupidx<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
groupnames |
Generate unque names for peak groups |
groupnames,xcmsEIC-method |
Generate unque names for peak groups |
groupnames,xcmsSet-method |
Generate unque names for peak groups |
groups |
Class xcmsSet, a class for preprocessing peak data |
groups,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
groups<- |
Class xcmsSet, a class for preprocessing peak data |
groups<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
groupval |
Extract a matrix of peak values for each group |
groupval,xcmsSet-method |
Extract a matrix of peak values for each group |
peaks |
Class xcmsSet, a class for preprocessing peak data |
peaks,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
peaks<- |
Class xcmsSet, a class for preprocessing peak data |
peaks<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
phenoData |
Class xcmsSet, a class for preprocessing peak data |
phenoData,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
phenoData<- |
Class xcmsSet, a class for preprocessing peak data |
phenoData<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
plot, plot-methods |
Plot extracted ion chromatograms from multiple files |
plot.xcmsEIC |
Plot extracted ion chromatograms from multiple files |
plotChrom |
Plot extracted ion chromatograms from the profile matrix |
plotChrom,xcmsRaw-method |
Plot extracted ion chromatograms from the profile matrix |
plotPeaks |
Plot a grid of a large number of peaks |
plotPeaks,xcmsRaw-method |
Plot a grid of a large number of peaks |
plotRaw |
Scatterplot of raw data points |
plotRaw,xcmsRaw-method |
Scatterplot of raw data points |
plotrt |
Plot retention time deviation profiles |
plotrt,xcmsSet-method |
Plot retention time deviation profiles |
plotScan |
Plot a single mass scan |
plotScan,xcmsRaw-method |
Plot a single mass scan |
plotSpec |
Plot mass spectra from the profile matrix |
plotSpec,xcmsRaw-method |
Plot mass spectra from the profile matrix |
plotSurf |
Plot profile matrix 3D surface using OpenGL |
plotSurf,xcmsRaw-method |
Plot profile matrix 3D surface using OpenGL |
plotTIC |
Plot total ion count |
plotTIC,xcmsRaw-method |
Plot total ion count |
plotTree |
Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
plotTree,xcmsFragments-method |
Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
profinfo |
Class xcmsSet, a class for preprocessing peak data |
profinfo,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
profinfo<- |
Class xcmsSet, a class for preprocessing peak data |
profinfo<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
profMedFilt |
Median filtering of the profile matrix |
profMedFilt,xcmsRaw-method |
Median filtering of the profile matrix |
profMethod |
Get and set method for generating profile data |
profMethod,xcmsRaw-method |
Get and set method for generating profile data |
profMethod<- |
Get and set method for generating profile data |
profMethod<-,xcmsRaw-method |
Get and set method for generating profile data |
profMz |
Class xcmsRaw, a class for handling raw data |
profMz,xcmsRaw-method |
Class xcmsRaw, a class for handling raw data |
profRange |
Specify a subset of profile mode data |
profRange,xcmsRaw-method |
Specify a subset of profile mode data |
profStep |
Get and set m/z step for generating profile data |
profStep,xcmsRaw-method |
Get and set m/z step for generating profile data |
profStep<- |
Get and set m/z step for generating profile data |
profStep<-,xcmsRaw-method |
Get and set m/z step for generating profile data |
rawEIC |
Get extracted ion chromatograms for specified m/z range |
rawEIC,xcmsRaw-method |
Get extracted ion chromatograms for specified m/z range |
rawMat |
Get a raw data matrix |
rawMat,xcmsRaw-method |
Get a raw data matrix |
rawMat-methods |
Get a raw data matrix |
retcor |
Correct retention time from different samples |
retcor,xcmsSet-method |
Correct retention time from different samples |
retcor-methods |
Correct retention time from different samples |
retcor.linear |
Align retention times across samples |
retcor.linear,xcmsSet-method |
Align retention times across samples |
retcor.loess |
Align retention times across samples |
retcor.loess,xcmsSet-method |
Align retention times across samples |
retcor.obiwarp |
Align retention times across samples with Obiwarp |
retcor.obiwarp,xcmsSet-method |
Align retention times across samples with Obiwarp |
retcor.peakgroups |
Align retention times across samples |
retcor.peakgroups,xcmsSet-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,xcmsRaw-method |
Class xcmsRaw, a class for handling raw data |
rtrange |
Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
rtrange,xcmsEIC-method |
Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
sampclass |
Class xcmsSet, a class for preprocessing peak data |
sampclass,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
sampclass<- |
Class xcmsSet, a class for preprocessing peak data |
sampclass<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
sampnames |
Get sample names |
sampnames,xcmsEIC-method |
Get sample names |
sampnames,xcmsSet-method |
Get sample names |
sampnames<- |
Class xcmsSet, a class for preprocessing peak data |
sampnames<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
score_fun |
Scoring for MS/MS spectra |
score_fun.cor |
Scoring for MS/MS spectra Via correlation |
score_fun.distMatrix |
Scoring for MS/MS spectra |
searchMetlin |
Search Metlin Online Database |
searchMetlin,xcmsFragments-method |
Search Metlin Online Database |
show,xcmsEIC-method |
Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
show,xcmsFragments-method |
Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data |
show,xcmsPeaks-method |
A matrix of peaks |
show,xcmsRaw-method |
Class xcmsRaw, a class for handling raw data |
show,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
simSearch |
Unrestricted precursor Metlin Search |
simSearch,xcmsFragments-method |
Unrestricted precursor Metlin Search |
sortMz |
Class xcmsRaw, a class for handling raw data |
sortMz,xcmsRaw-method |
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, split-methods |
Divide an xcmsSet object |
split.xcmsRaw |
Divide an xcmsRaw object |
split.xcmsSet |
Divide an xcmsSet object |
SSgauss |
Gaussian Model |