## ---- 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 #