Interactive Visualization of Integrated Differential Expression
and Differential Network Analysis for Biomarker Candidate
Selection Package
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Documentation for package ‘INDEED’ version 2.19.0
Help Pages
| INDEED-package | INDEED: A network-based method for cacner biomarker discovery. |
| choose_rho | Draw error curve |
| compute_cor | Compute the correlation |
| compute_dns | Calculate the differential network score |
| compute_par | Compute the partial correlation |
| INDEED | INDEED: A network-based method for cacner biomarker discovery. |
| loglik_ave | Create log likelihood error |
| Met_Group_GU | Group label. |
| Met_GU | GU cirrhosis (CIRR) and GU Hepatocellular carcinoma (HCC) data. |
| Met_name_GU | KEGG ID |
| network_display | Interactive Network Visualization |
| non_partial_cor | Non-partial correlaton analysis |
| partial_cor | Partial correlaton analysis |
| permutation_cor | Permutations to build a differential network based on correlation analysis |
| permutation_pc | Permutations to build differential network based on partial correlation analysis |
| permutation_thres | Calculate the positive and negative thresholds based on the permutation result |
| pvalue_logit | Obtain p-values using logistic regression |
| pvalue_M_GU | P-values obtained by differential expression (DE) analysis. |
| scale_range | Scale list of numbers |
| select_rho_partial | Data preprocessing for partial correlaton analysis |