## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, message = TRUE, warning = FALSE, cache = FALSE, fig.align = 'center', fig.width = 5, fig.height = 4, crop = NULL ) ## ----installation, eval=FALSE------------------------------------------------- # if(!requireNamespace('BiocManager', quietly = TRUE)) # install.packages('BiocManager') # # BiocManager::install("BioNERO") ## ----load_package------------------------------------------------------------- # Load package after installation library(BioNERO) set.seed(123) # for reproducibility ## ----------------------------------------------------------------------------- # Load example data set data(zma.se) # Preprocess the expression data final_exp <- exp_preprocess( zma.se, min_exp = 10, variance_filter = TRUE, n = 2000 ) ## ----load_tfs----------------------------------------------------------------- data(zma.tfs) head(zma.tfs) ## ----exp2grn, fig.small=TRUE-------------------------------------------------- # Using 10 trees for demonstration purposes. Use the default: 1000 grn <- exp2grn( exp = final_exp, regulators = zma.tfs$Gene, nTrees = 10 ) head(grn) ## ----genie3------------------------------------------------------------------- # Using 10 trees for demonstration purposes. Use the default: 1000 genie3 <- grn_infer( final_exp, method = "genie3", regulators = zma.tfs$Gene, nTrees = 10) head(genie3) dim(genie3) ## ----aracne------------------------------------------------------------------- aracne <- grn_infer(final_exp, method = "aracne", regulators = zma.tfs$Gene) head(aracne) dim(aracne) ## ----clr---------------------------------------------------------------------- clr <- grn_infer(final_exp, method = "clr", regulators = zma.tfs$Gene) head(clr) dim(clr) ## ----grn_combined------------------------------------------------------------- grn_list <- grn_combined(final_exp, regulators = zma.tfs$Gene, nTrees = 10) head(grn_list$genie3) head(grn_list$aracne) head(grn_list$clr) ## ----get_hubs----------------------------------------------------------------- hubs <- get_hubs_grn(grn) hubs ## ----plot_static, fig.height=4, fig.width=4----------------------------------- plot_grn(grn) ## ----plot_interactive--------------------------------------------------------- plot_grn(grn, interactive = TRUE, dim_interactive = c(500,500)) ## ----------------------------------------------------------------------------- sessionInfo()