R/INDEED.R

In ressomlab/INDEED: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

#' 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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