% 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().
}