Run CAMERA package with settings from the settings list (see
FEMsettings). Works both for LC and GC. Not meant to be called
directly by the user.
runCAMERA(xset, chrom = c("LC", "GC"), settings, polarity, quick = TRUE)
For LC, an
The type of chromatography. Either "LC" or "GC".
The subset of settigs contained into the "CAMERA" element of the settings list.
The polarity of the injection, used by CAMERA to look for common adducts.
Only relevant for LC data.
In the case of LC the function is used in data analysis and DB
creation. In the first case, it increases the level of the annotation
and it it, by default, run with
TRUE. For DB
creation, the grouping of the features into "pcgroups" (features with
similar retention time) is used to choose the features to be included
into the database. In this case camera is run with
quick determines whether or not the correlation
among the extracted ion chromatograms should be used to "validate" the
For GC data, only the grouping done by
groupFWHM is performed:
basically this clusters peaks with a similar retention time.
An annotated xcmsSet object (an object of class CAMERA).
Ron Wehrens and Pietro Franceschi
## Example of results data(LCresults) ## pre-compiled results LCresults$PeakTable
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