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 |
groupidx |
Class xcmsSet, a class for preprocessing peak data |
groupidx,xcmsSet-method |
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<-,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<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
plot |
Plot extracted ion chromatograms from multiple files |
plot,xcmsEIC-method |
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 |
profinfo |
Class xcmsSet, a class for preprocessing peak data |
profinfo,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
profinfo<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
profMedFilt |
Apply a median filter to the profile matrix |
profMedFilt,xcmsRaw-method |
Apply a median filter to the profile matrix |
profMethod |
Get and set method for generating profile data |
profMethod,xcmsRaw-method |
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<-,xcmsRaw-method |
Get and set m/z step for generating profile data |
sampclass |
Class xcmsSet, a class for preprocessing peak data |
sampclass,xcmsSet-method |
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<-,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
show,xcmsEIC-method |
Class xcmsEIC, a class for multi-sample extracted ion chromatograms |
show,xcmsRaw-method |
Class xcmsRaw, a class for handling raw data |
show,xcmsSet-method |
Class xcmsSet, a class for preprocessing peak data |
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.xcmsSet |
Divide an xcmsSet object |
SSgauss |
Gaussian Model |