## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # # install from bioconductor # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("cosmosR") # # # # install the newest (development) version from GitHub # # install.packages("remotes") # # install CARNIVAL from github # remotes::install_github("saezlab/CARNIVAL") # remotes::install_github("saezlab/cosmosR") ## ---- warning=FALSE, message=FALSE-------------------------------------------- library(cosmosR) ## ---- warning=FALSE, message=FALSE-------------------------------------------- CARNIVAL_options <- default_CARNIVAL_options(solver = "lpSolve") # To use CBC # CARNIVAL_options <- default_CARNIVAL_options(solver = "cbc") # CARNIVAL_options$solverPath <- "~/Documents/cbc" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05 # To use CPLEX: # CARNIVAL_options <- default_CARNIVAL_options(solver = "cplex") # CARNIVAL_options$solverPath <- "C:/Program Files/CPLEX_solver/cplex/bin/x64_win64/cplex.exe" # CARNIVAL_options$threads <- 2 # CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$timelimit <- 3600 ## ---- warning=FALSE, message=FALSE-------------------------------------------- data(toy_network) data(toy_signaling_input) data(toy_metabolic_input) data(toy_RNA) test_for <- preprocess_COSMOS_signaling_to_metabolism(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = TRUE, CARNIVAL_options = CARNIVAL_options) ## ---- warning=FALSE, message=FALSE-------------------------------------------- CARNIVAL_options$timelimit <- 14400 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 ## ---- warning=FALSE, message=FALSE-------------------------------------------- test_result_for <- run_COSMOS_signaling_to_metabolism(data = test_for, CARNIVAL_options = CARNIVAL_options) ## ---- warning=FALSE, message=FALSE-------------------------------------------- formated_result_for <- format_COSMOS_res(test_result_for) ## ---- warning=FALSE, message=FALSE-------------------------------------------- CARNIVAL_options$timelimit <- 3600 CARNIVAL_options$mipGAP <- 0.05 CARNIVAL_options$threads <- 2 ## ---- warning=FALSE, message=FALSE-------------------------------------------- test_back <- preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network, signaling_data = toy_signaling_input, metabolic_data = toy_metabolic_input, diff_expression_data = toy_RNA, maximum_network_depth = 15, remove_unexpressed_nodes = FALSE, CARNIVAL_options = CARNIVAL_options) ## ---- warning=FALSE, message=FALSE-------------------------------------------- CARNIVAL_options$timelimit <- 28800 test_result_back <- run_COSMOS_metabolism_to_signaling(data = test_back, CARNIVAL_options = CARNIVAL_options) ## ---- warning=FALSE, message=FALSE-------------------------------------------- formated_result_back <- format_COSMOS_res(test_result_back) ## ---- warning=FALSE, message=FALSE-------------------------------------------- full_sif <- as.data.frame(rbind(formated_result_for[[1]], formated_result_back[[1]])) full_sif <- full_sif[full_sif$Weight>0,] full_attributes <- as.data.frame(rbind(formated_result_for[[2]], formated_result_back[[2]])) full_sif <- unique(full_sif) full_attributes <- unique(full_attributes) ## ---- warning=FALSE, message=FALSE-------------------------------------------- network_plot <- display_node_neighboorhood(central_node = 'Metab__D-Glucitol_c', sif = full_sif, att = full_attributes, n = 7) network_plot ## ---- warning=FALSE, message=FALSE-------------------------------------------- sif_forward = formated_result_for[[1]] att_forward = formated_result_for[[2]] nodes_ORA = extract_nodes_for_ORA( sif = sif_forward, att = att_forward) ## ---- warning=FALSE, message=FALSE-------------------------------------------- sessionInfo()