Identification of Prognosis-Related Mutually Exclusive Modules

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Documentation for package ‘ProgModule’ version 0.1.0

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

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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