# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- 风格,回声= FALSE,结果= '飞机 '---------------------------------------- BiocStyle:减价 () ## ---- 设置中,回声= FALSE,消息= FALSE ----------------------------------------- 图书馆(MSstatsPTM) # #——安装、eval = FALSE ------------------------------------------------------ # devtools:: install_github(“tsunghengtsai / MSstatsPTM ") ## ---- 自由,eval = FALSE ---------------------------------------------------------- # 库(MSstatsPTM) # #——模拟 ----------------------------------------------------------------- # sim < - PTMsimulateExperiment (# nGroup = 2, nRep = 2, nProtein = 1, nSite = 2, nFeature = 5, #μ=列表(天车= 25、蛋白质= 25),#δ=列表(天车= c(0, 1),蛋白质= c (0,1)), # sRep =列表(天车= 0.2,蛋白质= 0.2),#说话=列表(天车= 0.05,蛋白质= 0.05)#)sim < PTMsimulateExperiment (nGroup = 2, nRep = 2, nProtein = 1, nSite = 2, nFeature = 5,logAbundance =列表(天车=列表(μ= 25,δ= c (0, 1), sRep = 0.2, = 0.05)说,蛋白质=列表(μ= 25,δ= c (0, 1), sRep = 0.2, = 0.05 ) ) ) ## ---- 数据结构 ----------------------------------------------------------- str (sim) # #——data-ptm ----------------------------------------------------------------- sim[[“天车 "]] ## ---- data-protein ------------------------------------------------------------- sim[[“蛋白质 "]] ## ---- fasta,eval = FALSE -------------------------------------------------------- # fas < tidyFasta (" https://www.uniprot.org/uniprot/P37840.fasta ") ## ---- 正常化,消息= FALSE --------------------------------------------- 规范化的< - PTMnormalize (sim,方法=“中值”)归一化# #——normalization-ref消息= FALSE ----------------------------------------- < -参考文献列表(天车= data.frame(运行= paste0 (R_, 1:4), adjLog2inty = c(2 2 0,0)),蛋白质= data.frame(运行= paste0 (R_, 1:4), adjLog2inty = c(3、1,0,0))) PTMnormalize (sim方法=“ref”,参参=)# #——总结,消息= FALSE --------------------------------------------- 总结了< - PTMsummarize(规范化)总结# #——估计,消息= FALSE ------------------------------------------------ 估计< - PTMestimate(总结)估计 ## ----------------------------------------------------------------------------- PTMcompareMeans(估计,控制=“G_1里面”,例= " G_2 ") ## ----------------------------------------------------------------------------- PTMcompareMeans(估计,控制=“G_1里面”,例=“G_2 adjProtein = TRUE) # #——会话 ------------------------------------------------------------------ sessionInfo ()