## ----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')