--- a
+++ b/vignettes/Introduction_to_INDEED.R
@@ -0,0 +1,39 @@
+## ----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)
+
+## ----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----------------------------------------------------------------
+#  result <- non_partial_cor(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU, method = "pearson",
+#                            p_val = pvalue_M_GU, permutation = 1000, permutation_thres = 0.05, fdr = TRUE)
+
+## ---- eval = F----------------------------------------------------------------
+#  pre_data <- select_rho_partial(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU,
+#                                 error_curve = TRUE)
+#  result <- partial_cor(data_list = pre_data, rho_group1 = 'min', rho_group2 = "min", p_val = pvalue_M_GU,
+#                        permutation = 1000, permutation_thres = 0.05, fdr = TRUE)
+
+## ---- eval = F----------------------------------------------------------------
+#  result <- non_partial_cor(data = Met_GU, class_label = Met_Group_GU, id = Met_name_GU, method = "pearson",
+#                            p_val = pvalue_M_GU, permutation = 1000, permutation_thres = 0.05, fdr = FALSE)
+#  network_display(result = result, nodesize= 'Node_Degree', nodecolor= 'Activity_Score',
+#                  edgewidth= FALSE, layout= 'nice')
+