cameraWrapper: cameraWrapper
In mjhelf/METABOseek: Metaboseek platform

cameraWrapper

R Documentation

cameraWrapper

Description

converts a XCMSnExp object to xcmsSet, then consecutively calls xsAnnotate, groupFWHM, groupCorr, findIsotopes and findAdducts from the CAMERA package, and finally adds an entry to its .processHistory slot.

Usage

cameraWrapper(
  xset,
  polarity = NULL,
  sigma = 6,
  perfwhm = 0.6,
  cor_eic_th = 0.75,
  pval = 0.05,
  maxcharge = 3,
  maxiso = 4,
  ppm = 5,
  mzabs = 0.01,
  minfrac = 0.5,
  filter = TRUE,
  workers = 1
)

Arguments

`xset`	a `XCMSnExp` object
`polarity`	passed on to `xsAnnotate()` and `findAdducts()`
`sigma`	passed on to `groupFWHM()`
`perfwhm`	passed on to `groupFWHM()`
`cor_eic_th`	passed on to `groupCorr()`
`pval`	passed on to `groupCorr()`
`maxcharge`	passed on to `findIsotopes()`
`maxiso`	passed on to `findIsotopes()`
`ppm`	passed on to `findIsotopes()` and `findAdducts()`
`mzabs`	passed on to `findIsotopes()` and `findAdducts()`
`minfrac`	passed on to `findIsotopes()`
`filter`	passed on to `findIsotopes()`
`workers`	number of workers, passed on to `xsAnnotate()` (as `nSlaves`)