# #——风格,回声= FALSE,结果=“黑名单”,消息= FALSE --------------------- BiocStyle:减价 () ## ---- 回声= FALSE,消息= FALSE ------------------------------------------- 库(BiocStyle ) ## ---- eval = FALSE ------------------------------------------------------------ # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) {# install.packages(“BiocManager ") # } # # (“MobilityTransformR BiocManager:安装 ") ## ---- eval = FALSE ------------------------------------------------------------ # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) {# install.packages(“BiocManager ") # } # # BiocManager::安装(“xcms”)# BiocManager::安装(“光谱 ") ## ---- 库,消息= FALSE,警告= FALSE ---------------------------------- # 负载所需的库库(MobilityTransformR)图书馆(xcms)图书馆(光谱)# #——数据,消息= FALSE ------------------------------------------------------ fl < - dir(系统。file("CE-MS"， package = "msdata")， full.names = TRUE) #加载mzXML数据与MSnBase raw_data <- readMSData(files = fl, mode = "onDisk") ## ----EOF标记，message=FALSE, warning=FALSE--------------------------------- # mz公差取决于MS质量精度公差<- 0.005 # [M+H]+的对乙酰amol:mz = 152.071154 mz_paracetamol <- c(152.071154 -耐受性，152.071154 +耐受性)mt_paracetamol <- c(600,900) marker_EIE <- raw_data |> filterMz(mz = mz_paracetamol) |> filtert (rt = mt_paracetamol) plot(色谱图(marker_EIE)， main = "Paracetamol EIE"， xlab = "迁移时间(sec)")#必要时调整mz和MT窗口## ----EOF标记getMT, message=FALSE，警告=FALSE--------------------------- #获取对乙酰氨基酚对乙酰氨基酚的MT <- getMtime(raw_data, mz = mz_paracetamol, MT = mt_paracetamol)对乙酰氨基酚## ----控告标记，message=FALSE，警告=FALSE-----------------------------普罗卡因<- data.frame("rtime" = c(450.239, 465.711)， "fileIdx" = c(1，2 ) ) ## ---- 消息= FALSE ----------------------------------------------------------- # 创建一个存储标记信息标记< - data.frame扑热息痛标记markerID < -“扑热息痛”标记美元流动性< - 0 # #——流动性,消息= FALSE -------------------------------------------------- procaineMobility < mobilityTransform (x =[1],普鲁卡因标志=标记[1],tR = 3/60, U = + 30,L = 800) procaineMobility # #——消息= FALSE ----------------------------------------------------------- 普鲁卡因markerID < -“普鲁卡因”普鲁卡因美元流动性< - procaineMobility标记< rbind(标记,普鲁卡因 ) ## ---- 消息= FALSE ----------------------------------------------------------- # 太OnDiskMSnExp对象转换mobility_data < - mobilityTransform (x = raw_data,标志=标记)# OnDiskMSnExp可以通过导出writeMSData,注意,#设置复制= FALSE,是很重要的(否则频谱顺序会错误)fl_mobility_data <- tempfile() writeMSData(filterFile(mobility_data, 1)， file = fl_mobility_data, copy =FALSE) ## ---- message=FALSE----------------------------------------------------------- #加载测试数据作为光谱对象spectra_data <- spectra (fl[1]， backend = MsBackendMzR()) spectra_mobility <- mobilityTransform(spectra_data, marker[marker$fileIdx == 1，) #转换后的数据可以再次导出为.mzML文件，以在xcms或#其他软件fl_mobility中使用<- tempfile() export(spectra_mobility, MsBackendMzR()， file = fl_mobility) ## ----移动转换后的数据，message=FALSE--------------------------------- #示例:从赖氨酸中提取离子电泳图(EIE) mz_lysine <- c(147.112806 - tolerance, 147.112806 + tolerance) mobilityRestriction <- c(1000,2500) #提取化合物lysine_EIE的离子电泳图<- mobility_data |> filterMz(mz = mz_lysine) |> filtert (rt = mobilityRestriction) plot(色谱(lysine_EIE)， main = expression(paste("µ"[eff]， " scale")， xlab = expression(paste("µ"[eff]， " ("mm"^2， "kV min")，")")))) #比较提取离子迁移时间刻度的电泳图lysine_mt_EIE <- raw_data |> filterMz(mz = mz_lysine) |> filtert (c(400,600)) plot(色谱(lysine_mt_EIE)， main = "Lysine EIE - MT刻度"，xlab = "MT (sec)") ## ----si----------------------------------------------------------------------- sessionInfo()