An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Documentation for package ‘INDEED’ version 1.2.0

INDEED-package	INDEED: A package for biomarker candidate prioritization.
choose_rho	Draw error curve
compute_cor	Compute the correlation
compute_dns	Calculate differential network score
compute_par	Compute the partial correlation
INDEED	INDEED: A package for biomarker candidate prioritization.
loglik_ave	Create log likelihood error function
Met_Group_GU	Group label.
Met_GU	GU CIRR and GU HCC combined .
Met_name_GU	KEGG ID
non_partial_cor	Non-partial correlaton analysis
partial_cor	Data preprocessing for partial correlaton analysis
permutation_cor	Permutations to build differential network using correlation
permutation_pc	Permutations to build differential network using partial correlation
permutation_thres	Calculate the positive and negative threshold based on the permutation result
pre_partial	Data preprocessing for partial correlaton analysis
pvalue_logit	Obtain p-values using logistic regression
pvalue_M_GU	P-values obtained by differential expression (DE) analysis.