# # # R代码从装饰图案的RMassBankNonstandard来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:RMassBankNonstandard。Rnw: 26 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 74)#库(xtable) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:RMassBankNonstandard。Rnw: 41-44 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(“RMassBank”)库(RMassBankData)库(gplots) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 3号代码块:RMassBankNonstandard。Rnw: 50-51 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #装饰图案(RMassBank) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:RMassBankNonstandard。Rnw: 71 - 78 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # RmbDefaultSettings () rmbo <——getOption (RMassBank) rmbo recalibrator < -列表(“MS1”=”调整。身份”、“一份“=”调整。身份”)选项(“RMassBank”= rmbo) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:RMassBankNonstandard。Rnw: 84 - 86 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # w < - loadMsmsWorkspace(执行(“结果/ pH_narcotics_RF。RData”,包= " RMassBankData ")) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:RMassBankNonstandard。Rnw: 90 - 91 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotRecalibration (w) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:RMassBankNonstandard。Rnw: 95 - 97 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # w@recalibratedSpecs[[1]]美元parentPeak [30:32,] w@recalibratedSpecs山峰美元[[1]][[1]](十五17,)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:RMassBankNonstandard。Rnw: 103 - 104 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # w <——msmsWorkflow (= w,步骤4)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:RMassBankNonstandard。Rnw: 110 - 112 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # w@recalibratedSpecs[[1]]美元parentPeak [30:32,] w@recalibratedSpecs山峰美元[[1]][[1]](十五17,)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:RMassBankNonstandard。Rnw: 130 - 150 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # RmbDefaultSettings () getOption (RMassBank) multiplicityFilter #美元处理更快,我们只使用3光谱/复合rmbo <——getOption (RMassBank) rmbo spectraList < -列表(列表(=“CID”模式,ces =“35%”, ce =“35%(名义)”res = 7500),列表(=“HCD”模式,ces =“15%”, ce =“15%(名义)”res = 7500),列表(=“HCD”模式,ces =“30%”, ce =“30%(名义)”, 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] ################################################### ### code chunk number 11: RMassBankNonstandard.Rnw:153-163 ################################################### w1 <- msmsWorkflow(w, mode="pH", steps=c(1)) # Here we artificially cut spectra out to make the workflow run faster for the vignette: w1@specs <- lapply(w1@specs, function(s) { s$childScans <- s$childScans[1:3] s$childHeaders <- s$childHeaders[1:3,] s$peaks <- s$peaks[1:3] s }) w1 <- msmsWorkflow(w1, mode="pH", steps=c(2:7)) ################################################### ### code chunk number 12: RMassBankNonstandard.Rnw:169-179 ################################################### 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@specs <- lapply(w2@specs, function(s) { s$childScans <- s$childScans[1:3] s$childHeaders <- s$childHeaders[1:3,] s$peaks <- s$peaks[1:3] s }) w2 <- msmsWorkflow(w2, mode="pH", steps=c(2:7)) ################################################### ### code chunk number 13: RMassBankNonstandard.Rnw:185-187 ################################################### wTotal <- combineMultiplicities(c(w1, w2)) wTotal <- msmsWorkflow(wTotal, steps=8, mode="pH", archivename = "output") ################################################### ### code chunk number 14: RMassBankNonstandard.Rnw:192-194 ################################################### mb <- newMbWorkspace(wTotal) # [...] load lists, execute workflow etc. ################################################### ### code chunk number 15: RMassBankNonstandard.Rnw:201-202 ################################################### sessionInfo()