# Identification of Prognosis-Related Mutually Exclusive Modules

## Documentation for package ‘ProgModule’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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