MI                      Calculate mutual information.
candidate_module        candidate_module, candidate module
final_candidate_module
                        final_candidate_module, Final candidate modules
get_Pvalue_S            Get perturbed p-value.
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_mut_status          Converts MAF file into mutation matrix.
get_mut_survivalresult
                        Plot Kaplan-Meier survival curve.
get_mutual_module       Extract the mutually exclusive module.
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_univarCox_result    Get univarCox result.
local_network           local_network, local network gene set
maf_data                maf_data, MAF file
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
