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## ----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()
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