getAnnotationLC: Get LC annotation

Description

Main function for the annotation of an xcmsSet or CAMERA object. This function is not meant to be called directly. Use runLC instead.

Usage

getAnnotationLC(xs, settings, DB, errf)

Arguments

The xcmsSet (or CAMERA) object to be annotated.

settings

The subset of settings contained into the match2DB elements of the settings list. See the help of FEMsettings for details.

The database used within AnnotateTable for the annotation of the peaklist. See the help of FLCDBtest for details.

errf

The file containing the error function used to predict the m/z tolerance. See the help of AnnotateTable for details.

Value

A list with two elements. raw is the complete output of AnnotateTable. for_table is a data.frame which summarizes the outputs of the annotation (see AnnotateTable) and it is included in the output of the runLC main function.

Details

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 asmaxo - 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 AnnotateTable. If xs contains more than one sample, the intensity is the maximum intensity of each feature across all the samples.

References

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).