## ----warning=FALSE, message=FALSE--------------------------------------------- library(SPONGE) ## ----eval=FALSE--------------------------------------------------------------- # head(gene_expr) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(gene_expr[1:5,1:8]) ## ----eval=FALSE--------------------------------------------------------------- # head(mir_expr) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(mir_expr[1:5,1:5]) ## ----eval = FALSE------------------------------------------------------------- # head(targetscan_symbol) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(targetscan_symbol[1:5,1:5]) ## ----warning=FALSE,message=FALSE---------------------------------------------- genes_miRNA_candidates <- sponge_gene_miRNA_interaction_filter( gene_expr = gene_expr, mir_expr = mir_expr, mir_predicted_targets = targetscan_symbol) ## ----------------------------------------------------------------------------- genes_miRNA_candidates[1:2] ## ----message=FALSE, warning=FALSE--------------------------------------------- ceRNA_interactions <- sponge(gene_expr = gene_expr, mir_expr = mir_expr, mir_interactions = genes_miRNA_candidates) ## ----eval=FALSE--------------------------------------------------------------- # head(ceRNA_interactions) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(head(ceRNA_interactions)) ## ----message=FALSE, warning=FALSE--------------------------------------------- mscor_null_model <- sponge_build_null_model(number_of_datasets = 100, number_of_samples = nrow(gene_expr)) ## ----fig.width = 12, fig.height = 7------------------------------------------- sponge_plot_simulation_results(mscor_null_model) ## ----message=FALSE, error=FALSE----------------------------------------------- ceRNA_interactions_sign <- sponge_compute_p_values(sponge_result = ceRNA_interactions, null_model = mscor_null_model) ## ----eval=FALSE--------------------------------------------------------------- # head(ceRNA_interactions_sign) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(head(ceRNA_interactions_sign)) ## ----------------------------------------------------------------------------- ceRNA_interactions_fdr <- ceRNA_interactions_sign[which(ceRNA_interactions_sign$p.adj < 0.2),] ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable(head(ceRNA_interactions_fdr)) ## ----------------------------------------------------------------------------- sponge_plot_network(ceRNA_interactions_fdr, genes_miRNA_candidates) ## ----------------------------------------------------------------------------- network_centralities <- sponge_node_centralities(ceRNA_interactions_fdr) ## ----------------------------------------------------------------------------- ceRNA_interactions_fdr_weight <- ceRNA_interactions_fdr ceRNA_interactions_fdr_weight$weight <- -log10(ceRNA_interactions_fdr$p.adj) weighted_network_centralities <- sponge_node_centralities(ceRNA_interactions_fdr) ## ----fig.height = 7, fig.width = 7, warning=FALSE,message=FALSE,error=FALSE---- sponge_plot_network_centralities(weighted_network_centralities, top = 1) ## ----fig.height = 7, fig.width = 7, warning=FALSE,message=FALSE,error=FALSE---- sponge_plot_network_centralities(weighted_network_centralities, measure = "btw", top = 1) ## ----eval=FALSE--------------------------------------------------------------- # library(doParallel) # library(foreach) # # num.of.cores <- 2 #many more on a compute cluster # # #if you want to use logging # #logging.file <- "where_my_log_file_should_go.log" # logging.file <- NULL # # cl <- makeCluster(num.of.cores, outfile=logging.file) # registerDoParallel(cl) # # genes_miRNA_candidates <- sponge_gene_miRNA_interaction_filter( # gene_expr = gene_expr, # mir_expr = mir_expr, # mir_predicted_targets = targetscan_symbol) # # ceRNA_interactions <- sponge( # gene_expr = gene_expr, # mir_expr = mir_expr, # mir_interactions = genes_miRNA_candidates) # # stopCluster(cl) # ## ----eval = FALSE------------------------------------------------------------- # library("BiocParallel") # register(DoparParam(), default = TRUE) ## ----eval = FALSE------------------------------------------------------------- # library(clustermq) # register_dopar_cmq(n_jobs=2) ## ----message=FALSE, warning=FALSE, error=FALSE-------------------------------- more_covariance_matrices <- sample_zero_mscor_cov(m = 1, number_of_solutions = 10, gene_gene_correlation = 0.5) ## ----message=FALSE, warning=FALSE, error=FALSE, fig.width = 7, fig.height = 7---- mscor_coefficients <- sample_zero_mscor_data(cov_matrices = more_covariance_matrices, number_of_samples = 200, number_of_datasets = 100) hist(unlist(mscor_coefficients), main = "Random distribution of mscor coefficients")