#' INDEED: A network-based method for cacner biomarker discovery.

#'

#' 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().

#'

#' @docType package

#' @name INDEED

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