## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width=8, fig.height=8 ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("MSstatsLiP") ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(MSstatsLiP) library(tidyverse) library(data.table) ## ----------------------------------------------------------------------------- ## Read in raw data files head(LiPRawData) head(TrPRawData) ## ----------------------------------------------------------------------------- ## Run converter MSstatsLiP_data <- SpectronauttoMSstatsLiPFormat(LiPRawData, "../inst/extdata/ExampleFastaFile.fasta", TrPRawData, use_log_file = FALSE, append = FALSE) head(MSstatsLiP_data[["LiP"]]) head(MSstatsLiP_data[["TrP"]]) ## Make conditions match MSstatsLiP_data[["LiP"]][MSstatsLiP_data[["LiP"]]$Condition == "Control", "Condition"] = "Ctrl" MSstatsLiP_data[["TrP"]]$Condition = substr(MSstatsLiP_data[["TrP"]]$Condition, 1, nchar(MSstatsLiP_data[["TrP"]]$Condition)-1) ## ----------------------------------------------------------------------------- MSstatsLiP_Summarized <- dataSummarizationLiP(MSstatsLiP_data, MBimpute = FALSE, use_log_file = FALSE, append = FALSE) names(MSstatsLiP_Summarized[["LiP"]]) lip_protein_data <- MSstatsLiP_Summarized[["LiP"]]$ProteinLevelData trp_protein_data <- MSstatsLiP_Summarized[["TrP"]]$ProteinLevelData head(lip_protein_data) head(trp_protein_data) ## ----------------------------------------------------------------------------- trypticHistogramLiP(MSstatsLiP_Summarized, "../inst/extdata/ExampleFastaFile.fasta", color_scale = "bright", address = FALSE) ## ----------------------------------------------------------------------------- correlationPlotLiP(MSstatsLiP_Summarized, address = FALSE) ## ----------------------------------------------------------------------------- MSstatsLiP_Summarized[["LiP"]]$FeatureLevelData %>% group_by(FEATURE, GROUP) %>% summarize(cv = sd(INTENSITY) / mean(INTENSITY)) %>% ggplot() + geom_violin(aes(x = GROUP, y = cv, fill = GROUP)) + labs(title = "Coefficient of Variation between Condtions", y = "Coefficient of Variation", x = "Conditon") ## ----------------------------------------------------------------------------- ## Quality Control Plot dataProcessPlotsLiP(MSstatsLiP_Summarized, type = 'QCPLOT', which.Peptide = "allonly", address = FALSE) ## ----------------------------------------------------------------------------- dataProcessPlotsLiP(MSstatsLiP_Summarized, type = 'ProfilePlot', which.Peptide = c("P14164_ILQNDLK"), address = FALSE) ## ----------------------------------------------------------------------------- PCAPlotLiP(MSstatsLiP_Summarized, bar.plot = FALSE, protein.pca = FALSE, comparison.pca = TRUE, which.comparison = c("Ctrl", "Osmo"), address=FALSE) PCAPlotLiP(MSstatsLiP_Summarized, bar.plot = FALSE, protein.pca = TRUE, comparison.pca = FALSE, which.pep = c("P14164_ILQNDLK", "P17891_ALQLINQDDADIIGGRDR"), address=FALSE) ## ----------------------------------------------------------------------------- feature_data <- data.table::copy(MSstatsLiP_Summarized$LiP$FeatureLevelData) data.table::setnames(feature_data, c("PEPTIDE", "PROTEIN"), c("PeptideSequence", "ProteinName")) feature_data$PeptideSequence <- substr(feature_data$PeptideSequence, 1, nchar(as.character( feature_data$PeptideSequence)) - 2) calculateTrypticity(feature_data, "../inst/extdata/ExampleFastaFile.fasta") MSstatsLiP_Summarized$LiP$FeatureLevelData%>% rename(PeptideSequence=PEPTIDE, ProteinName=PROTEIN)%>% mutate(PeptideSequence=substr(PeptideSequence, 1, nchar(as.character(PeptideSequence))-2) ) %>% calculateTrypticity("../inst/extdata/ExampleFastaFile.fasta") ## ----------------------------------------------------------------------------- MSstatsLiP_model <- groupComparisonLiP(MSstatsLiP_Summarized, fasta = "../inst/extdata/ExampleFastaFile.fasta", use_log_file = FALSE, append = FALSE) lip_model <- MSstatsLiP_model[["LiP.Model"]] trp_model <- MSstatsLiP_model[["TrP.Model"]] adj_lip_model <- MSstatsLiP_model[["Adjusted.LiP.Model"]] head(lip_model) head(trp_model) head(adj_lip_model) ## Number of significant adjusted lip peptides adj_lip_model %>% filter(adj.pvalue < .05) %>% nrow() ## ----------------------------------------------------------------------------- groupComparisonPlotsLiP(MSstatsLiP_model, type = "VolcanoPlot", address = FALSE) ## ----------------------------------------------------------------------------- groupComparisonPlotsLiP(MSstatsLiP_model, type = "HEATMAP", numProtein=50, address = FALSE) ## ----------------------------------------------------------------------------- StructuralBarcodePlotLiP(MSstatsLiP_model, "../inst/extdata/ExampleFastaFile.fasta", model_type = "Adjusted", which.prot = c("P53858"), address = FALSE) ## ----calculate accessibility, message=FALSE, warning=FALSE, echo=TRUE,include=TRUE---- Accessibility = calculateProteolyticResistance(MSstatsLiP_Summarized, "../inst/extdata/ExampleFastaFile.fasta", differential_analysis = TRUE) Accessibility$RunLevelData ## ----Barplot of protease resistance of aSynuclein (monomer - M and fibril - F), message=FALSE, warning=FALSE, fig.height=2, fig.width=10,echo=TRUE,include=TRUE---- ResistanceBarcodePlotLiP(Accessibility, "../inst/extdata/ExampleFastaFile.fasta", which.prot = "P14164", which.condition = "Osmo", address = FALSE) ResistanceBarcodePlotLiP(Accessibility, "../inst/extdata/ExampleFastaFile.fasta", differential_analysis = TRUE, which.prot = "P53858", which.condition = "Osmo", address = FALSE)