## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, warning= FALSE, message=FALSE------------------------------------- library(ceRNAnetsim) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ceRNAnetsim") ## ----------------------------------------------------------------------------- data("TCGA_E9_A1N5_tumor") data("TCGA_E9_A1N5_normal") data("mirtarbasegene") data("TCGA_E9_A1N5_mirnanormal") ## ----------------------------------------------------------------------------- TCGA_E9_A1N5_mirnanormal %>% inner_join(mirtarbasegene, by= "miRNA") %>% inner_join(TCGA_E9_A1N5_normal, by = c("Target"= "external_gene_name")) %>% select(Target, miRNA, total_read, gene_expression) %>% distinct() -> TCGA_E9_A1N5_mirnagene ## ----------------------------------------------------------------------------- TCGA_E9_A1N5_tumor%>% inner_join(TCGA_E9_A1N5_normal, by= "external_gene_name")%>% select(patient = patient.x, external_gene_name, tumor_exp = gene_expression.x, normal_exp = gene_expression.y)%>% distinct()%>% inner_join(TCGA_E9_A1N5_mirnagene, by = c("external_gene_name"= "Target"))%>% filter(tumor_exp != 0, normal_exp != 0)%>% mutate(FC= tumor_exp/normal_exp)%>% filter(external_gene_name== "HIST1H3H") #HIST1H3H: interacts with various miRNA in dataset, so we can say that HIST1H3H is non-isolated competing element and increases to 30-fold. ## ----------------------------------------------------------------------------- TCGA_E9_A1N5_tumor%>% inner_join(TCGA_E9_A1N5_normal, by= "external_gene_name") %>% select(patient = patient.x, external_gene_name, tumor_exp = gene_expression.x, normal_exp = gene_expression.y) %>% distinct() %>% inner_join(TCGA_E9_A1N5_mirnagene, by = c("external_gene_name"= "Target")) %>% filter(tumor_exp != 0, normal_exp != 0) %>% mutate(FC= tumor_exp/normal_exp) %>% filter(external_gene_name == "ACTB") #ACTB: interacts with various miRNA in dataset, so ACTB is not isolated node in network and increases to 1.87-fold. ## ----------------------------------------------------------------------------- TCGA_E9_A1N5_mirnagene %>% group_by(Target) %>% mutate(gene_expression= max(gene_expression)) %>% distinct() %>% ungroup() -> TCGA_E9_A1N5_mirnagene TCGA_E9_A1N5_mirnagene%>% filter(gene_expression > 10)->TCGA_E9_A1N5_mirnagene ## ----warning=FALSE, eval=FALSE------------------------------------------------ # TCGA_E9_A1N5_mirnagene %>% # priming_graph(competing_count = gene_expression, # miRNA_count = total_read)%>% # calc_perturbation(node_name= "ACTB", cycle=10, how= 1.87,limit = 0.1) ## ----warning=FALSE, eval=FALSE------------------------------------------------ # TCGA_E9_A1N5_mirnagene %>% # priming_graph(competing_count = gene_expression, # miRNA_count = total_read)%>% # calc_perturbation(node_name= "ACTB", cycle=10, how= 30,limit = 0.1) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()