metaMS (version 1.8.0)

runCAMERA: 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).

Value

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

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.

See Also

annotate, groupFWHM