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


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Documentation for package ‘INDEED’ version 1.0.1

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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.