## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ) ## ----installation, eval=FALSE------------------------------------------------- # if(!requireNamespace('BiocManager', quietly = TRUE)) # install.packages('BiocManager') # BiocManager::install("cogeqc") ## ----load_package, message = FALSE-------------------------------------------- # Load package after installation library(cogeqc) set.seed(123) # for reproducibility ## ----data_description--------------------------------------------------------- # Load synteny network for data(synnet) head(synnet) ## ----assess_synnet------------------------------------------------------------ assess_synnet(synnet) ## ----assess_list-------------------------------------------------------------- # Simulate networks net1 <- synnet net2 <- synnet[-sample(1:10000, 500), ] net3 <- synnet[-sample(1:10000, 1000), ] synnet_list <- list( net1 = net1, net2 = net2, net3 = net3 ) # Assess original network + 2 simulations synnet_assesment <- assess_synnet_list(synnet_list) synnet_assesment # Determine the best network synnet_assesment$Network[which.max(synnet_assesment$Score)] ## ----session_info------------------------------------------------------------- sessioninfo::session_info()