wrap_camera: Wraps CAMERA
In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description Usage Arguments Value Examples

Run a simple CAMERA workflow with user defined input parameters and return xsAnnotate objects

1	wrap_camera(xcms.obj, CAMERA.par, IonMode)

`xcms.obj`	an `xcmsSet` object that has had peak picking, retention time alignment, peak grouping, and imputing missing values performed.
`CAMERA.par`	a single-row data frame with 9 variables containing CAMERA parameters. Must include columns `"perfwhm"`,`"sigma"`,`"minfrac"`, `"mzabs"`,`"maxiso"`,`"corval_eic"`,`"corval_exp"`,`"pval"`, `"mzabs.1"`.
`IonMode`	a character string defining the ionization mode. Must be one of `c("Positive","Negative")`.

two grouped xsannotate objects mz1setpos,anposGa without and with annotated isotopes and ion adducts and fragments, respectively.

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {
file <- system.file("extdata","XCMS_objects_Pos.Rdata", package =
"lcmsfishdata") # is case sensitive on Linux
load(file, envir = environment())
file2 <- system.file("extdata","Best_CAMERA_parameters_positive.csv", package
= "lcmsfishdata")  # is case sensitive on Linux
CAMERA.par <- read.table(file2, header = TRUE, sep = ",")

## Not run: 

#Runs CAMERA. This requires access to raw datafiles and won't work with
#lcmsfishdata. Better to use your own data here.
test <- wrap_camera(xcms.obj = xset4, CAMERA.par = CAMERA.par, IonMode = "Positive")

## End(Not run)

}