| 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 |