## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=8, fig.height=8 ) ## ---- message=FALSE, warning=FALSE-------------------------------------------- library(MSstatsPTM) ## ---- eval = FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("MSstatsPTM") ## ----raw_data_ptm, eval = FALSE----------------------------------------------- # # Run MSstatsPTM converter with modified and unmodified datasets. # raw.input <- MaxQtoMSstatsPTMFormat(raw_ptm_df, annotation, evidence_file, # proteinGroupsfile) ## ----raw_data, eval = FALSE--------------------------------------------------- # # Add site into ProteinName column # raw_ptm_df$ProteinName <- paste(raw_ptm_df$ProteinName, # raw_ptm_df$Site, sep = "_") # # # Run MSstats Converters # PTM.data <- MaxQtoMSstatsTMTFormat(raw_ptm_df) # PROTEIN.data <- MaxQtoMSstatsTMTFormat(raw_protein_df) # # # Combine into one list # raw.input <- list(PTM = PTM.data, # PROTEIN = PROTEIN.data) ## ----------------------------------------------------------------------------- head(raw.input.tmt$PTM) head(raw.input.tmt$PROTEIN) ## ----summarize, echo=FALSE, message=FALSE, warning=FALSE---------------------- MSstatsPTM.summary <- dataSummarizationPTM_TMT(raw.input.tmt, verbose = FALSE) ## ----show_summ---------------------------------------------------------------- head(MSstatsPTM.summary$PTM$ProteinLevelData) head(MSstatsPTM.summary$PROTEIN$ProteinLevelData) ## ----qcplot, message=FALSE, warning=FALSE------------------------------------- dataProcessPlotsPTM(MSstatsPTM.summary, type = 'QCPLOT', which.PTM = "allonly", address = FALSE) ## ----profileplot, message=FALSE, warning=FALSE-------------------------------- dataProcessPlotsPTM(MSstatsPTM.summary, type = 'PROFILEPLOT', which.Protein = c("Protein_12"), address = FALSE) ## ----model, message=FALSE, warning=FALSE-------------------------------------- # Specify contrast matrix comparison <- matrix(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) # Set the names of each row row.names(comparison)<-c('1-4', '2-5', '3-6', '1-3', '2-3', '4-6', '5-6') colnames(comparison) <- c('Condition_1','Condition_2','Condition_3', 'Condition_4','Condition_5','Condition_6') MSstatsPTM.model <- groupComparisonPTM(MSstatsPTM.summary, data.type = "TMT", contrast.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)