## ----environment, echo=FALSE, message=FALSE, warning=FALSE----------------- library("topdownr") library("BiocStyle") ## ----citation, echo=FALSE, results="asis"---------------------------------- ct <- format(citation("topdownr"), "textVersion") cat(gsub("DOI: *(.*)$", "DOI: [\\1](https://doi.org/\\1)", ct), "\n") ## ----writeMethodXml, eval=FALSE-------------------------------------------- # library("topdownr") # # ## Create MS1 settings # ms1 <- expandMs1Conditions( # FirstMass=400, # LastMass=1200, # Microscans=as.integer(10) # ) # # ## Set TargetMass # targetMz <- cbind(mz=c(560.6, 700.5, 933.7), z=rep(1, 3)) # # ## Set common settings # common <- list( # OrbitrapResolution="R120K", # IsolationWindow=1, # MaxITTimeInMS=200, # Microscans=as.integer(40), # AgcTarget=c(1e5, 5e5, 1e6) # ) # # ## Create settings for different fragmentation conditions # cid <- expandTms2Conditions( # MassList=targetMz, # common, # ActivationType="CID", # CIDCollisionEnergy=seq(7, 35, 7) # ) # hcd <- expandTms2Conditions( # MassList=targetMz, # common, # ActivationType="HCD", # HCDCollisionEnergy=seq(7, 35, 7) # ) # etd <- expandTms2Conditions( # MassList=targetMz, # common, # ActivationType="ETD", # ETDReactionTime=as.double(1:2) # ) # etcid <- expandTms2Conditions( # MassList=targetMz, # common, # ActivationType="ETD", # ETDReactionTime=as.double(1:2), # ETDSupplementalActivation="ETciD", # ETDSupplementalActivationEnergy=as.double(1:2) # ) # uvpd <- expandTms2Conditions( # MassList=targetMz, # common, # ActivationType="UVPD" # ) # # ## Create experiments with all combinations of the above settings # ## for fragment optimisation # exps <- createExperimentsFragmentOptimisation( # ms1=ms1, cid, hcd, etd, etcid, uvpd, # groupBy=c("AgcTarget", "replication"), nMs2perMs1=10, scanDuration=0.5, # replications=2, randomise=TRUE # ) # # ## Write experiments to xml files # writeMethodXmls(exps=exps) # # ## Run XMLMethodChanger # runXmlMethodChanger( # modificationXml=list.files(pattern="^method.*\\.xml$"), # templateMeth="TMS2IndependentTemplateForTD.meth", # executable="path\\to\\XmlMethodChanger.exe" # ) ## ----ScanHeadsman, eval=FALSE---------------------------------------------- # runScanHeadsman( # path="path\\to\\raw-files", # executable="path\\to\\ScanHeadsman.exe" # ) ## ----sessioninfo----------------------------------------------------------- sessionInfo()