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 |