## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----message= FALSE, warning=FALSE-------------------------------------------- library(ceRNAnetsim) library(png) ## ---- message=FALSE, warning= FALSE, eval=FALSE------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ceRNAnetsim") ## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'---- data("minsamp") minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression) %>% update_how("Gene4",2) %>% simulate_vis(title = "Minsamp: Common element as trigger", cycle = 15) minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression) %>% update_how("Gene4",2) %>% simulate(cycle = 5) ## ----------------------------------------------------------------------------- data("midsamp") midsamp ## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'---- midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_how("Gene17",2) %>% simulate_vis(title = "Midsamp: Gene with higher degree as trigger", 15) ## ----------------------------------------------------------------------------- midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_how("Gene2",2) %>% simulate(50) %>% find_iteration(limit=0) ## ----------------------------------------------------------------------------- data("midsamp_new_counts") midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_variables(current_counts = midsamp_new_counts) %>% simulate(50) %>% find_iteration(limit=0) ## ---- fig.align='center', fig.width=5, fig.height=3, dpi= 120----------------- midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_how("Gene17",2) %>% simulate(50) %>% find_iteration(limit=0) ## ---- fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'---- midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_how("Gene17", 2) %>% simulate_vis(title = "Midsamp: Gene17 2 fold increase, 25 cycles", 25) ## ---- fig.align='center', fig.height=5, fig.width=6, warning=FALSE, message=FALSE, fig.show='hide'---- midsamp %>% priming_graph(Gene_expression, miRNA_expression) %>% update_how("Gene17", 2) %>% simulate_vis(title = "Midsamp: Gene17 2 fold increase, 6 cycles", 6, threshold = 1) ## ----------------------------------------------------------------------------- midsamp %>% priming_graph(competing_count = Gene_expression, miRNA_count = miRNA_expression, aff_factor = c(Energy,seeds), deg_factor = targeting_region) %>% calc_perturbation("Gene17", 3, cycle = 30, limit = 0.1) ## ----------------------------------------------------------------------------- primed_mid <- midsamp %>% priming_graph(competing_count = Gene_expression, miRNA_count = miRNA_expression, aff_factor = c(Energy,seeds), deg_factor = targeting_region) ## ---- eval=FALSE-------------------------------------------------------------- # # for parallel processing # # future::plan(multiprocess) # # seq(2,10) %>% # rlang::set_names() %>% # furrr::future_map_dfr(~ primed_mid %>% calc_perturbation("Gene17", .x, cycle = 30, limit = 0.1), .id="fold_change") ## ---- warning=FALSE----------------------------------------------------------- midsamp %>% priming_graph(competing_count = Gene_expression, miRNA_count = miRNA_expression, aff_factor = c(Energy,seeds), deg_factor = targeting_region) %>% find_node_perturbation(how = 3, cycle = 4, limit = 0.1)%>% select(name, perturbation_efficiency, perturbed_count) ## ----------------------------------------------------------------------------- midsamp %>% priming_graph(competing_count = Gene_expression, miRNA_count = miRNA_expression, aff_factor = c(Energy,seeds), deg_factor = targeting_region) %>% find_node_perturbation(how = 3, cycle = 4, limit = 0.1, fast=5)%>% select(name, perturbation_efficiency, perturbed_count) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()