final_signature         final_signature, the final prognosis-related
                        pathways
gene_Ucox               gene_Ucox
gene_Ucox_res           gene_Ucox_res, the univariate Cox regression
                        result of candidate genes.
gene_symbol_Entrez      gene_symbol_Entrez, the genes' symbol and
                        ENTREZID
get_Entrez_ID           Convert gene symbol to Entrez_Gene_ID
get_MultivariateCox_result
                        Perform the multivariate Cox regression
get_Oncoplots           draw an GenePathwayOncoplots
get_final_signature     Identify the candidate prognosis-related
                        pathways
get_km_survival_curve   Plot Kaplan-Meier survival curve.
get_mut_status          Converts MAF file into mutation matrix
get_pfs_score           Calculates the pathway-based mutation
                        accumulate perturbation score
get_response_plot       Plot the response column diagram
get_risk_score          Calculates the risk score for patients
get_roc_curve           Plot the ROC curve
get_sam_cla             get_sam_cla
get_univarCox_result    Perform the univariate Cox regression analysis.
km_data                 km_data
maf_data                maf_data
maffile                 maffile
mut_num                 mut_num
mut_sam                 mut_sam
mut_sample              mut_sample
mut_status              mut_status
newspia                 newspia
path_Ucox_mul           path_Ucox_mul
path_Ucox_mul_res       path_Ucox_mul_res
path_cox_data           path_cox_data
path_gene               path_gene
pfs_score               pfs_score
response                response
roc_data                roc_data, the data frame use for ploting ROC
                        curve
sig                     sig
sur                     sur
symbol_Entrez           symbol_Entrez
