cameraWrapper: cameraWrapper

View source: R/Functions_xcmsRunner.R

cameraWrapperR 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)

Value

an xsAnnotate object


mjhelf/METABOseek documentation built on April 27, 2022, 5:13 p.m.