| candidate_module | candidate_module, candidate module |
| final_candidate_module | final_candidate_module, Final candidate modules |
| get_candidate_module | Get candidate module. |
| get_final_module | Get final module. |
| get_local_network | Extract the local networks from the PPI network. |
| get_lollipopPlot | Draw an lollipopPlot for module genes |
| get_mutual_module | Extract the mutually exclusive module. |
| get_mut_status | Converts MAF file into mutation matrix. |
| get_mut_survivalresult | Plot Kaplan-Meier survival curve. |
| get_oncoplots | Draw a waterfall plot of mutated genes involved in the module |
| get_plotMutInteract | Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways. |
| get_Pvalue_S | Get perturbed p-value. |
| get_univarCox_result | Get univarCox result. |
| local_network | local_network, local network gene set |
| maf_data | maf_data, MAF file |
| MI | Calculate mutual information. |
| module | module, gene set |
| mut_status | mut_status, mutations matrix |
| net | net, network |
| plotMutInteract_moduledata | plotMutInteract_moduledata |
| plotMutInteract_mutdata | plotMutInteract_mutdata |
| subnet | subnet, network |
| univarCox_result | univarCox_result |