# #设置,包括= FALSE ----------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,评论= " # > ",fig.width = 8, fig.height = 8 ) ## ---- 消息= FALSE,警告= FALSE -------------------------------------------- 库(MSstatsPTM ) ## ---- eval = FALSE ------------------------------------------------------------ # 如果(!requireNamespace("BiocManager"， quiet = TRUE)) # install.packages("BiocManager") ## BiocManager::install("MSstatsPTM") ## ----raw_data_ptm, eval = FALSE----------------------------------------------- ##使用修改和未修改的数据集运行MSstatsPTM转换器。#生。input <- MaxQtoMSstatsPTMFormat(raw_ptm_df, annotation, evidence_file， # proteinGroupsfile) ## ----raw_data, eval = FALSE--------------------------------------------------- ##添加站点到ProteinName列# raw_ptm_df$ProteinName <- paste(raw_ptm_df$ProteinName， # raw_ptm_df$ site, sep = "_") ## #运行MSstats Converters # PTM。data <- MaxQtoMSstatsTMTFormat(raw_ptm_df) #蛋白。data <- MaxQtoMSstatsTMTFormat(raw_protein_df)input <- list(PTM = PTM。数据,# = PROTEIN.data蛋白质 ) ## ----------------------------------------------------------------------------- 头(raw.input.tmt天车美元)头(raw.input.tmt蛋白质美元)# #——总而言之,呼应= FALSE,消息= FALSE,警告= FALSE ---------------------- MSstatsPTM。summary <- dataSummarizationPTM_TMT(raw.input. tmt)tmt verbose = FALSE) # #——show_summ ---------------------------------------------------------------- 头(MSstatsPTM.summary天车ProteinLevelData美元)头(MSstatsPTM.summary蛋白质ProteinLevelData美元)# #——qcplot消息= FALSE,警告= FALSE ------------------------------------- dataProcessPlotsPTM (MSstatsPTM。summary, type = 'QCPLOT'，即。天车= "都不过”,地址= FALSE) # #——profileplot消息= FALSE,警告= FALSE -------------------------------- dataProcessPlotsPTM (MSstatsPTM。summary, type = 'PROFILEPLOT'。蛋白质= c(“Protein_12”)、地址= FALSE) # #——模型,消息= FALSE,警告= FALSE -------------------------------------- # 指定的对比矩阵比较< -矩阵(c (1 0 0 1 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1), nrow = 7, ncol = 6, byrow = TRUE) #集的每一行的名字row.names(比较)< - c(“1 - 4”,“2 - 5”、“6”,“1 - 3”、“2 - 3”、“4”,“5 - 6”)colnames(比较)< - c(‘Condition_1’,‘Condition_2’,‘Condition_3’,“Condition_4”、“Condition_5”、“Condition_6”)MSstatsPTM。model <- groupComparisonPTM(MSstatsPTM. msc)摘要,数据。type = "TMT"，对比。matrix = comparison) head(MSstatsPTM.model$PTM.Model) head(MSstatsPTM.model$PROTEIN.Model) head(MSstatsPTM.model$ADJUSTED.Model) ## ----volcano, message=FALSE, warning=FALSE------------------------------------ groupComparisonPlotsPTM(data = MSstatsPTM.model, type = "VolcanoPlot", which.Comparison = c('1-4'), which.PTM = 1:50, address=FALSE) ## ----meatmap, message=FALSE, warning=FALSE------------------------------------ groupComparisonPlotsPTM(data = MSstatsPTM.model, type = "Heatmap", which.PTM = 1:49, address=FALSE)