c.xcmsSet |
Combine xcmsSet objects |
cdfpaths |
Class xcmsSet, a class for preprocessing peak data |
colMax |
Find row and column maximum values |
diffreport |
Create report of analyte differences |
etg |
Empirically Transformed Gaussian function |
fillPeaks |
Integrate areas of missing peaks |
findPeaks |
Feature detection in the chromatographic time domain |
getEIC |
Get extracted ion chromatograms for specified m/z ranges |
getPeaks |
Get peak intensities for specified regions |
getScan |
Get m/z and intensity values for a single mass scan |
getSpec |
Get average m/z and intensity values for multiple mass scans |
group |
Group peaks from different samples together |
groupidx |
Class xcmsSet, a class for preprocessing peak data |
groups |
Class xcmsSet, a class for preprocessing peak data |
groupval |
Extract a matrix of peak values for each group |
image.xcmsRaw |
Plot log intensity image of a xcmsRaw object |
medianFilter |
Apply a median filter to a matrix |
peaks |
Class xcmsSet, a class for preprocessing peak data |
plotChrom |
Plot extracted ion chromatograms from the profile matrix |
plotEIC |
Plot a list of EICs for each sample |
plotPeaks |
Plot a grid of a large number of peaks |
plotRaw |
Scatterplot of raw data points |
plotrt |
Plot retention time deviation profiles |
plotScan |
Plot a single mass scan |
plotSpec |
Plot mass spectra from the profile matrix |
plotSurf |
Plot profile matrix 3D surface using OpenGL |
plotTIC |
Plot total ion count |
profinfo |
Class xcmsSet, a class for preprocessing peak data |
profMedFilt |
Apply a median filter to the profile matrix |
profMethod |
Get and set method for generating profile data |
profMz |
Class xcmsRaw, a class for handling raw data |
profRange |
Specify a subset of profile mode data |
profStep |
Get and set m/z step for generating profile data |
retcor |
Align retention times across samples |
retexp |
Set retention time window to a specified width |
revMz |
Class xcmsRaw, a class for handling raw data |
rowMax |
Find row and column maximum values |
sampclass |
Class xcmsSet, a class for preprocessing peak data |
sampnames |
Class xcmsSet, a class for preprocessing peak data |
sortMz |
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 |
xcmsRaw |
Constructor for xcmsRaw objects which reads NetCDF files |
xcmsRaw-class |
Class xcmsRaw, a class for handling raw data |
xcmsSet |
Constructor for xcmsSet objects which finds peaks in NetCDF files |
xcmsSet-class |
Class xcmsSet, a class for preprocessing peak data |