## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Rtpca") ## ----Load, message=FALSE------------------------------------------------------ library(Rtpca) ## ----message=FALSE, warning=FALSE--------------------------------------------- library(TPP) ## ----------------------------------------------------------------------------- data("hdacTR_smallExample") ## ----------------------------------------------------------------------------- set.seed(123) random_proteins <- sample(hdacTR_data[[1]]$gene_name, 300) ## ----------------------------------------------------------------------------- hdacTR_data_fil <- lapply(hdacTR_data, function(temp_df){ filter(temp_df, gene_name %in% random_proteins) }) ## ----------------------------------------------------------------------------- trData <- tpptrImport(configTable = hdacTR_config, data = hdacTR_data_fil) ## ----------------------------------------------------------------------------- data("string_ppi_df") string_ppi_df ## ----------------------------------------------------------------------------- string_ppi_cs_950_df <- string_ppi_df %>% filter(combined_score >= 950 ) vehTPCA <- runTPCA( objList = trData, ppiAnno = string_ppi_cs_950_df ) ## ----------------------------------------------------------------------------- data("ori_et_al_complexes_df") ori_et_al_complexes_df ## ----------------------------------------------------------------------------- vehComplexTPCA <- runTPCA( objList = trData, complexAnno = ori_et_al_complexes_df, minCount = 2 ) ## ----------------------------------------------------------------------------- plotPPiRoc(vehTPCA, computeAUC = TRUE) ## ----------------------------------------------------------------------------- plotComplexRoc(vehComplexTPCA, computeAUC = TRUE) ## ----------------------------------------------------------------------------- diffTPCA <- runDiffTPCA( objList = trData[1:2], contrastList = trData[3:4], ctrlCondName = "DMSO", contrastCondName = "Panobinostat", ppiAnno = string_ppi_cs_950_df) ## ----------------------------------------------------------------------------- plotDiffTpcaVolcano( diffTPCA, setXLim = TRUE, xlimit = c(-0.5, 0.5)) ## ----------------------------------------------------------------------------- head(diffTpcaResultTable(diffTPCA) %>% arrange(p_value) %>% dplyr::select(pair, rssC1_rssC2, f_stat, p_value, p_adj)) ## ----------------------------------------------------------------------------- plotPPiProfiles(diffTPCA, pair = c("KPNA6", "KPNB1")) ## ----------------------------------------------------------------------------- sessionInfo()