INDEED: INDEED: A package for biomarker candidate prioritization.

In kg737/INDEED_Patch: Integrated Differential Expression and Differential Network Analysis (INDEED)

Description

The INDEED package provides an important functions below: select_rho_partial, partial_cor, non_partial_cor and network_display.

select_rho_partial function

select_rho_partial function preprocess 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

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 rho of their choice and number of permutations (default 1000), p-value is optional, the result of score table and differential network will be returned

non_partial_cor function

non_partial_cor function performs correlation analysis based on user input data, class label, p-value, sample id, number of permutations, and method (default pearson) p value is optional, the result of score table and differential network will be returned

network_display function

A tool to assist in the network visualization of the results from INDEED functions patial_cor() and non_partial_cor().

networkVis function

An interactive tool to assist in the network visualization of the results from INDEED functions patial_cor() and non_partial_cor().

kg737/INDEED_Patch documentation built on May 22, 2019, 6:32 p.m.