runCAMERA: The CAMERA element in the metaMS pipeline

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

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

Examples

## Example of results
  data(LCresults) ## pre-compiled results
  LCresults$PeakTable

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.