## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval = F-----------------------------------------------------------------
# # install.packages("devtools")
# devtools::install_github("ressomlab/INDEED")

## ----eval = F-----------------------------------------------------------------
# # load INDEED
# library(INDEED)
# # Loading required package: glasso

## ----dataset, eval = F--------------------------------------------------------
# # Data matrix contains the expression levels of 39 metabolites from 120 subjects
# # (6 metabolites and 10 subjects are shown)
# head(Met_GU[, 1:10])
# # Group label for each subject (40 subjects are shown)
# Met_Group_GU[1:40]
# # Metabolite KEGG IDs (10 metabolites are shown)
# Met_name_GU[1:10]
# 

## ----eval = F-----------------------------------------------------------------
# non_partial_cor(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU, method = "spearman")

## ----eval = F-----------------------------------------------------------------
# pre_data <- select_rho_partial(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU,
#                                error_curve = "YES")
# result <- partial_cor(data_list = pre_data, rho_group1 = 'min', rho_group2 = "min",
#                       permutation = 1000, p_val = pvalue_M_GU, permutation_thres = 0.05)

## ----eval = F-----------------------------------------------------------------
# network_display(results = result, nodesize= 'Node_Degree', nodecolor= 'Activity_Score',
#                 edgewidth= 'NO', layout= 'nice')