## ----eval=FALSE---------------------------------------------------------------
#  
#  msconvert ORB35017raw.RAW --mzXML
#  msconvert ORB35017raw.RAW --mzXML
#  

## ----eval=FALSE---------------------------------------------------------------
#  # load the package
#  library(adductData)

## ----quiet=T, eval=FALSE------------------------------------------------------
#  
#  rtDevModelling(MS2Dir = system.file("extdata", package = "adductData"),
#  nCores=4, runOrder = paste0(system.file("extdata", package = "adductomicsR"),
#  '/runOrder.csv'))
#  
#  #access the files using ExperimentHub
#  library(ExperimentHub)
#  eh  = ExperimentHub()
#  temp = query(eh, 'adductData')
#  temp
#  

## ----quiet=T, eval=FALSE------------------------------------------------------
#  
#  adductQuant(nCores=4, targTable=paste0(system.file("extdata",
#  package = "adductomicsR"),'/exampletargTable2.csv'), intStdRtDrift=30,
#  rtDevModels=paste0(system.file("extdata", package = "adductData"),
#  '/rtDevModels.RData'),
#  filePaths=list.files(system.file("extdata", package = "adductData"),
#      pattern=".mzXML", all.files=FALSE,full.names=TRUE),
#  quantObject=NULL,indivAdduct=NULL,maxPpm=5,minSimScore=0.8,spikeScans=1,
#  minPeakHeight=100,maxRtDrift=20,maxRtWindow=240,isoWindow=80,
#  hkPeptide='LVNEVTEFAK', gaussAlpha=16)
#  
#  #access the files using ExperimentHub
#  library(ExperimentHub)
#  eh  = ExperimentHub()
#  temp = query(eh, 'adductData')
#  temp
#