# #——回声= FALSE --------------------------------------------------------- 选项(宽度= 74 ) ## ----------------------------------------------------------------------- 库(RMassBank ) ## ----------------------------------------------------------------------- 库(RMassBankData) # # - eval = TRUE ---------------------------------------------------------- file.copy(执行(“列表/ NarcoticsDataset.csv”、包=“RMassBankData”),”。/ Compoundlist.csv ") ## ---- eval = TRUE ---------------------------------------------------------- RmbSettingsTemplate(“mysettings.ini ") ## ---- 回声= TRUE, eval = TRUE ------------------------------------------------ loadRmbSettings(“mysettings.ini ") ## ----------------------------------------------------------------------- w < - newMsmsWorkspace () ## ----------------------------------------------------------------------- < - list.files(系统文件。文件("spectra"， package="RMassBankData")， "。mzML"， full.names = TRUE) basename(files) #为了让这里的工作流程更快，我们只使用了2个复合:w@files < -文件[1:2 ] ## ----------------------------------------------------------------------- loadList(“。/ Compoundlist.csv ") ## ---- eval = TRUE,无花果= TRUE ------------------------------------------------- w < msmsWorkflow (w模式=“pH”,步骤= c (1:4), archivename = " pH_narcotics ") ## ---- eval = FALSE --------------------------------------------------------- # plotRecalibration (w) # # - eval = FALSE --------------------------------------------------------- # w < msmsWorkflow (w模式=“pH”,步骤= 1)# w < - msmsWorkflow (w模式=“pH”,步骤= 2)# w < - msmsWorkflow (w模式=“pH”步骤= 3)# #等。# # - eval = FALSE --------------------------------------------------------- # 拉普兰人(w@spectra函数(s) s@found) # # - eval = FALSE --------------------------------------------------------- # findProgress (w) # # - eval = TRUE ---------------------------------------------------------- # 在真正评估工作流,我们做以下:#我们运行步骤1到3，从存储的工作流#加载重新校准曲线，并使用该曲线重新校准数据。storedW <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF. "RData”,包= " RMassBankData ")) ## ---- 无花果= TRUE ----------------------------------------------------------- # 刚从#显示校准曲线计算完整的数据集:storedW < - msmsWorkflow (storedW模式=“pH”,步骤= 4)#将校准复制到工作区w和应用#(没有图显示)w@rc < - storedW@parent@rc w@rc.ms1 < storedW@parent@rc.ms1 w < msmsWorkflow (w模式=“pH”,步骤= 4,archivename =“pH_narcotics newRecalibration = FALSE ) ## ----------------------------------------------------------------------- w < msmsWorkflow (w模式=“pH”,步骤= c (8),archivename = " pH_narcotics ") ## ---- eval = FALSE --------------------------------------------------------- # archiveResults (w,文件名 ) ## ----------------------------------------------------------------------- < - mb < - newMbWorkspace (w) mb resetInfolists (mb) mb < - loadInfolists (mb,系统。file("infolists_incomplete", package="RMassBankData")) ## ----eval=FALSE--------------------------------------------------------- # mb <- resetInfolists(mb) # mb <- loadInfolists(mb, my_folder_with_csv_infolists_inside) ## ----eval=FALSE--------------------------------------------------------- # mb <- addPeaks(mb, my_corrected_Failpeaks.csv) ## ----echo=TRUE,eval=TRUE------------------------------------------------ mb <- mbWorkflow(mb, infolist_path="./Narcotics_infolist.csv") ## ----eval=FALSE--------------------------------------------------------- # mb <- resetInfolists(mb) # mb <- loadInfolists(mb, my_folder_with_csv_infolists_inside) ## ----------------------------------------------------------------------- mb <- resetInfolists(mb) mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData")) ## ----eval=TRUE,echo=TRUE------------------------------------------------ mb <- mbWorkflow(mb) ## ----------------------------------------------------------------------- sessionInfo()