## ----setup, cache = F, echo = FALSE----------------------------------------
knitr::opts_chunk$set(error = TRUE)

## ----load_data-------------------------------------------------------------
require("netboost")
data("tcga_aml_meth_rna_chr18", package = "netboost")
dim(tcga_aml_meth_rna_chr18)

## ----netboost_run----------------------------------------------------------
results <- netboost(datan = tcga_aml_meth_rna_chr18, stepno = 20L, 
soft_power = 3L, min_cluster_size = 10L, n_pc = 2, scale = TRUE, ME_diss_thres = 0.25) 

## ----results---------------------------------------------------------------
names(results)
colnames(results$MEs)

## ----variance--------------------------------------------------------------
results$var_explained[,1:5]

## ----module_members--------------------------------------------------------
results$names[results$colors==10]

## ----plot------------------------------------------------------------------
set.seed(123)
nb_plot_dendro(nb_summary = results, labels = FALSE, colorsrandom = TRUE)

## ----transfer--------------------------------------------------------------
    ME_transfer <- nb_transfer(nb_summary = results, 
    new_data = tcga_aml_meth_rna_chr18, scale = TRUE)
    all(round(results$MEs, 12) == round(ME_transfer, 12))

## ----sessionInfo-----------------------------------------------------------
sessionInfo()
warnings()