Package 'xcms' - Bioconductor
Package 'xcms' - Bioconductor
Package 'xcms' - Bioconductor
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38 peakTable-methods<br />
peakTable-methods<br />
Create report of aligned peak intensities<br />
Description<br />
Create a report showing all aligned peaks.<br />
Arguments<br />
Details<br />
Value<br />
object<br />
filebase<br />
the xcmsSet object<br />
base file name to save report, .tsv file and _eic will be appended to this name<br />
for the tabular report and EIC directory, respectively. if blank nothing will be<br />
saved<br />
... arguments passed down to groupval, which provides the actual intensities.<br />
This method handles creation of summary reports similar to diffreport. It returns a summary<br />
report that can optionally be written out to a tab-separated file.<br />
If a base file name is provided, the report (see Value section) will be saved to a tab separated file.<br />
A data frame with the following columns:<br />
mz<br />
mzmin<br />
mzmax<br />
rt<br />
rtmin<br />
rtmax<br />
npeaks<br />
median m/z of peaks in the group<br />
minimum m/z of peaks in the group<br />
maximum m/z of peaks in the group<br />
median retention time of peaks in the group<br />
minimum retention time of peaks in the group<br />
maximum retention time of peaks in the group<br />
number of peaks assigned to the group<br />
Sample Classes number samples from each sample class represented in the group<br />
... one column for every sample class<br />
Sample Names<br />
integrated intensity value for every sample<br />
... one column for every sample<br />
Methods<br />
See Also<br />
object = "xcmsSet" peakTable(object, filebase = character(), ...)<br />
xcmsSet-class,
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