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ProgModule (version 0.1.0)

Identification of Prognosis-Related Mutually Exclusive Modules

Description

A novel tool to identify candidate driver modules for predicting the prognosis of patients by integrating exclusive coverage of mutations with clinical characteristics in cancer.

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Version

Install

install.packages('ProgModule')

Monthly Downloads

118

Version

0.1.0

License

GPL (>= 2)

Maintainer

Junwei Han

Last Published

May 16th, 2024

Functions in ProgModule (0.1.0)

net

net, network
get_mutual_module

Extract the mutually exclusive module.
subnet

subnet, network
get_oncoplots

Draw a waterfall plot of mutated genes involved in the module
plotMutInteract_mutdata

plotMutInteract_mutdata
plotMutInteract_moduledata

plotMutInteract_moduledata
final_candidate_module

final_candidate_module, Final candidate modules
MI

Calculate mutual information.
get_final_module

Get final module.
get_lollipopPlot

Draw an lollipopPlot for module genes
get_mut_survivalresult

Plot Kaplan-Meier survival curve.
get_candidate_module

Get candidate module.
get_local_network

Extract the local networks from the PPI network.
get_mut_status

Converts MAF file into mutation matrix.
get_Pvalue_S

Get perturbed p-value.
candidate_module

candidate_module, candidate module
mut_status

mut_status, mutations matrix
module

module, gene set
maf_data

maf_data, MAF file
local_network

local_network, local network gene set
get_univarCox_result

Get univarCox result.
univarCox_result

univarCox_result
get_plotMutInteract

Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways.