runCAMERA {metaMS} | R Documentation

## The CAMERA element in the metaMS pipeline

### Description

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.

### Usage

    runCAMERA(xset, chrom = c("LC", "GC"), settings, polarity, quick = TRUE)

### Arguments

`xset` | For LC, an `xcmsSet` object; for GC, a list of `xcmsSet` objects.
`chrom` | The type of chromatography. Either "LC" or "GC".
`settings` | The subset of settigs contained into the "CAMERA" element of the settings list.
`polarity` | The polarity of the injection, used by CAMERA to look for common adducts.
`quick` | Only relevant for LC data. If `TRUE`, CAMERA runs only `groupFWHM` and `findIsotopes`. If `FALSE`, correlations between EICs are calculated and used for grouping (which can take some time).

### Details

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 `quick` = `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` = `FALSE`: `quick` determines whether or not the correlation among the extracted ion chromatograms should be used to "validate" the pcgroups.

For GC data, only the grouping done by `groupFWHM` is performed: basically this clusters peaks with a similar retention time.

### Value

An annotated xcmsSet object (an object of class CAMERA).

### Author(s)

Ron Wehrens and Pietro Franceschi

### See Also

`annotate`, `groupFWHM`

[Package metaMS version 1.22.0 Index]