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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/INDEED.R
+\docType{package}
+\name{INDEED}
+\alias{INDEED}
+\title{INDEED: A network-based method for cacner biomarker discovery.}
+\description{
+The INDEED R package provides important functions as shown below:
+non_partial_cor(), select_rho_partial(), partial_cor(), and network_display().
+}
+\section{non_partial_cor function}{
+
+non_partial_cor function performs typical correlation analysis
+based on user input data, class label, p-value, sample id,
+number of permutations, and the method (default pearson)
+p value is optional,
+the result of score table and differential network will be returned
+}
+
+\section{select_rho_partial function}{
+
+select_rho_partial function preprocesses data for partical correlation analysis,
+the result contains list of preprocessed data and rho values and
+error plot for user to choose desired rho value for graphical lasso
+}
+
+\section{partial_cor function}{
+
+partial_cor function performs partical correlation analysis
+based on user input preprocessed list from select_rho_partial step
+and the rho choosing method or values of their choice
+and number of permutations (default 1000), p-value is optional,
+the result of score table and differential network will be returned
+}
+
+\section{network_display function}{
+
+A function to assist in the network visualization of the result from INDEED functions 
+non_partial_cor() and patial_cor().
+}
+