View source: R/getAnnotationLC.R
Main function for the annotation of an xcmsSet or CAMERA
object. This function is not meant to be called directly. Use
getAnnotationLC(xs, settings, DB, errf)
The xcmsSet (or CAMERA) object to be annotated.
The subset of settings contained into the match2DB elements of the
settings list. See the help of
The database used within
The file containing the error function used to predict the m/z
tolerance. See the help of
The function extracts from the
xs object a Peaktable with the
intensities of the features across all the samples. Since this
Peaktable is meant to be used only for annotation (and not for
subsequent statistical analysis), the intensities are expressed
maxo - the absolute maximum of the signal over the detected
chromatographic peak (see the documentation of xcms for more
details). Within the function the peaktable is converted into a matrix
in the form
(mz,rt,I) used by
xs contains more than one sample, the intensity is the maximum
intensity of each feature across all the samples.
A list with two elements.
raw is the complete output of
for_table is a
summarizes the outputs of the annotation (see
and it is included in the output of the
runLC main function.
N. Shahaf, P. Franceschi, P. Arapitsas, I. Rogachev, U. Vrhovsek and R. Wehrens: "Constructing a mass measurement error surface to improve automatic annotations in liquid chromatography/mass spectrometry based metabolomics". Rapid Communications in Mass Spectrometry, 27(21), 2425 (2013).
## Example of results data(LCresults) ## pre-compiled results LCresults$PeakTable
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