## ----echo=FALSE--------------------------------------------------------- options(width=74) ## ----echo=FALSE--------------------------------------------------------- library("RMassBank") library("RMassBankData") library("gplots") ## ----eval=FALSE--------------------------------------------------------- # vignette("RMassBank") ## ----------------------------------------------------------------------- RmbDefaultSettings() rmbo <- getOption("RMassBank") rmbo$recalibrator <- list( "MS1" = "recalibrate.identity", "MS2" = "recalibrate.identity" ) options("RMassBank" = rmbo) ## ----------------------------------------------------------------------- w <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData", package="RMassBankData")) ## ----fig=TRUE----------------------------------------------------------- recal <- makeRecalibration(w@parent, recalibrateBy = rmbo$recalibrateBy, recalibrateMS1 = rmbo$recalibrateMS1, recalibrator = list(MS1="recalibrate.loess",MS2="recalibrate.loess"), recalibrateMS1Window = 15) w@rc <- recal$rc w@rc.ms1 <- recal$rc.ms1 w@parent <- w plotRecalibration(w) ## ----------------------------------------------------------------------- w@spectra[[1]]@parent@mz[30:32] w@spectra[[1]]@children[[1]]@mz[15:17] ## ----fig=TRUE----------------------------------------------------------- w <- msmsWorkflow(w, steps=4) ## ----------------------------------------------------------------------- w@spectra[[1]]@parent@mz[30:32] w@spectra[[1]]@children[[1]]@mz[15:17] ## ----------------------------------------------------------------------- RmbDefaultSettings() getOption("RMassBank")$multiplicityFilter # to make processing faster, we only use 3 spectra per compound rmbo <- getOption("RMassBank") rmbo$spectraList <- list( list(mode="CID", ces = "35%", ce = "35 % (nominal)", res = 7500), list(mode="HCD", ces = "15%", ce = "15 % (nominal)", res = 7500), list(mode="HCD", ces = "30%", ce = "30 % (nominal)", res = 7500) ) options(RMassBank = rmbo) loadList(system.file("list/NarcoticsDataset.csv", package="RMassBankData")) w <- newMsmsWorkspace() files <- list.files(system.file("spectra", package="RMassBankData"), ".mzML", full.names = TRUE) w@files <- files[1:2] ## ----------------------------------------------------------------------- w1 <- msmsWorkflow(w, mode="pH", steps=c(1)) # Here we artificially cut spectra out to make the workflow run faster for the vignette: w1@spectra <- as(lapply(w1@spectra, function(s) { s@children <- s@children[1:3] s }),"SimpleList") w1 <- msmsWorkflow(w1, mode="pH", steps=c(2:7)) ## ----------------------------------------------------------------------- w2 <- msmsWorkflow(w, mode="pH", steps=c(1), confirmMode = 1) # Here we artificially cut spectra out to make the workflow run faster for the vignette: w2@spectra <- as(lapply(w2@spectra, function(s) { s@children <- s@children[1:3] s }),"SimpleList") w2 <- msmsWorkflow(w2, mode="pH", steps=c(2:7)) ## ----------------------------------------------------------------------- wTotal <- combineMultiplicities(c(w1, w2)) wTotal <- msmsWorkflow(wTotal, steps=8, mode="pH", archivename = "output") ## ----------------------------------------------------------------------- mb <- newMbWorkspace(wTotal) # [...] load lists, execute workflow etc. ## ----------------------------------------------------------------------- sessionInfo()