getAnnotationLC {metaMS} | R Documentation

## 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

`xs` | 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.
`DB` | 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.

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

### 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.

### Author(s)

Pietro Franceschi

### 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).

### See Also

`AnnotateTable`, `LCDBtest`, `FEMsettings`

[Package metaMS version 1.22.0 Index]