## ----echo=FALSE--------------------------------------------------------- options(width=74) ## ----------------------------------------------------------------------- library(RMassBank) library(RMassBankData) ## ----echo=TRUE,eval=TRUE------------------------------------------------ RmbDefaultSettings() rmbo <- getOption("RMassBank") rmbo$spectraList <- list( list(mode="CID", ces="10eV", ce="10eV", res=12000), list(mode="CID", ces="20eV", ce="20eV", res=12000) ) rmbo$multiplicityFilter <- 1 rmbo$annotations$instrument <- "Bruker micrOTOFq" rmbo$annotations$instrument_type <- "LC-ESI-QTOF" rmbo$recalibrator$MS1 <- "recalibrate.identity" rmbo$recalibrator$MS2 <- "recalibrate.identity" options("RMassBank" = rmbo) ## ----------------------------------------------------------------------- msmsList <- newMsmsWorkspace() ## ----------------------------------------------------------------------- msmsList@files <- list.files(system.file("spectra.Glucolesquerellin", package = "RMassBankData"), "Glucolesquerellin.*mzML", full.names=TRUE) ## ----------------------------------------------------------------------- loadList(system.file("list/PlantDataset.csv",package="RMassBankData")) ## ----eval=TRUE---------------------------------------------------------- Args <- list(method="centWave", peakwidth=c(5,12), prefilter=c(0,0), ppm=25, snthr=2) ## ----echo=FALSE,eval=TRUE----------------------------------------------- par(mfcol=c(2,2)) ## ----eval=TRUE, fig=TRUE------------------------------------------------ msmsList <- msmsRead(msmsList, files= msmsList@files, readMethod = "xcms", mode = "mH", Args = Args, plots = TRUE) msmsList <- msmsWorkflow(msmsList, steps=2:8, mode="mH", readMethod="xcms") ## ----------------------------------------------------------------------- mb <- newMbWorkspace(msmsList) mb <- resetInfolists(mb) mb <- loadInfolist(mb,system.file("infolists/PlantDataset.csv", package = "RMassBankData")) # Step mb <- mbWorkflow(mb, steps=1:8) ## ----eval=TRUE---------------------------------------------------------- msmsPeaklist <- newMsmsWorkspace() msmsPeaklist@files <- list.files(system.file("spectra.Glucolesquerellin", package = "RMassBankData"), "Glucolesquerellin.*csv", full.names=TRUE) msmsPeaklist <- msmsWorkflow(msmsPeaklist, steps=1:8, mode="mH", readMethod="peaklist") ## ----------------------------------------------------------------------- sessionInfo()