## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----pressure, echo=FALSE, fig.align='center', fig.width=6, fig.height=5, dpi=120---- knitr::include_graphics("gifs/model_vignette.png") ## ----setup, message= FALSE, warning=FALSE------------------------------------- library(ceRNAnetsim) ## ----Installation, eval = FALSE----------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ceRNAnetsim") ## ----echo=TRUE---------------------------------------------------------------- data("minsamp") minsamp %>% select(1:4) ## ----message= FALSE, warning=FALSE, echo=TRUE--------------------------------- data("minsamp") minsamp %>% select(competing, Competing_expression) %>% distinct() -> gene_expression ## ----------------------------------------------------------------------------- gene_expression ## ----message= FALSE, warning=FALSE, echo=TRUE--------------------------------- minsamp %>% select(miRNA, miRNA_expression) %>% distinct() -> mirna_expression ## ----------------------------------------------------------------------------- mirna_expression ## ----message= FALSE, warning=FALSE, echo=TRUE--------------------------------- minsamp %>% select(competing, miRNA) -> interaction_simple ## ----------------------------------------------------------------------------- interaction_simple ## ----------------------------------------------------------------------------- interaction_simple %>% inner_join(gene_expression, by = "competing") %>% inner_join(mirna_expression, "miRNA") -> basic_data basic_data ## ----------------------------------------------------------------------------- #Convertion of dataset to graph. priming_graph(basic_data, competing_count = Competing_expression, miRNA_count =miRNA_expression) ## ----------------------------------------------------------------------------- priming_graph(basic_data, competing_count = Competing_expression, miRNA_count =miRNA_expression) %>% update_how(node_name = "Gene2", how=2) ## ----------------------------------------------------------------------------- priming_graph(basic_data, competing_count = Competing_expression, miRNA_count =miRNA_expression) %>% update_how(node_name = "Gene2", how=2) %>% simulate(cycle = 5) ## ----------------------------------------------------------------------------- priming_graph(basic_data, competing_count = Competing_expression, miRNA_count =miRNA_expression) %>% update_how(node_name = "Gene2", how=2) %>% simulate(cycle = 5)%>% as_tibble()%>% select(name, initial_count, count_current) ## ----------------------------------------------------------------------------- priming_graph(basic_data, competing_count = Competing_expression, miRNA_count =miRNA_expression) %>% update_how(node_name = "Gene2", how=0) %>% simulate(cycle = 5) ## ----------------------------------------------------------------------------- minsamp ## ----------------------------------------------------------------------------- priming_graph(minsamp, competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) ## ----results='hold'----------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how(node_name = "Gene4", how = 2) %>% activate(edges)%>% # following line is just for focusing on necessary # columns to see the change in edge data select(3:4,comp_count_pre,comp_count_current) ## ----------------------------------------------------------------------------- data(new_counts) new_counts ## ----------------------------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_variables(current_counts = new_counts) ## ----------------------------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how("Gene4", how = 2) # OR # minsamp %>% # priming_graph(competing_count = Competing_expression, # miRNA_count = miRNA_expression, # aff_factor = c(energy, seed_type), # deg_factor = region) %>% # update_variables(current_counts = new_counts) ## ----echo=FALSE, fig.align='center', fig.width=10, fig.height=8, dpi=120------ knitr::include_graphics("gifs/small_sample_chunk10.png") ## ----------------------------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how("Gene4", how = 2) %>% simulate(cycle=10) #threshold with default 0. ## ----------------------------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how("Gene4", how = 2) %>% simulate(cycle=10) %>% activate(edges) %>% #from tidygraph package select(comp_count_list, mirna_count_list) %>% as_tibble() ## ----echo=FALSE, warning=FALSE, message=FALSE--------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how("Gene4", how = 2) %>% simulate(cycle=10) %>% activate(edges) %>% #from tidygraph package select(comp_count_list, mirna_count_list) %>% as_tibble() %>% filter(from==4, to==7) %>% pull(comp_count_list) %>% .[[1]] %>% round() ## ----------------------------------------------------------------------------- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_how("Gene4", how = 2) %>% simulate(cycle=3, threshold = 1) ## ----fig.height=4, fig.width=5, warning=FALSE, dpi= 120, fig.align='center'---- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% vis_graph(title = "Minsamp initial Graph") ## ----fig.height=4, fig.width=5, warning=FALSE, dpi= 120, fig.align='center'---- minsamp %>% priming_graph(competing_count = Competing_expression, miRNA_count = miRNA_expression, aff_factor = c(energy, seed_type), deg_factor = region) %>% update_variables(current_counts = new_counts) %>% simulate(3) %>% vis_graph(title = "Minsamp Graph After 3 Iteration") ## ----fig.height=4, fig.width=5, warning=FALSE, message=FALSE, eval=FALSE------ # minsamp %>% # priming_graph(competing_count = Competing_expression, # miRNA_count = miRNA_expression, # aff_factor = c(energy, seed_type), # deg_factor = region) %>% # update_variables(current_counts = new_counts) %>% # simulate_vis(3, title = "Minsamp Graph After Each Iteration") ## ----sessioninfo-------------------------------------------------------------- sessionInfo()