final_signature |
final_signature, the final prognosis-related pathways |
gene_symbol_Entrez |
gene_symbol_Entrez, the genes' symbol and ENTREZID |
gene_Ucox |
gene_Ucox |
gene_Ucox_res |
gene_Ucox_res, the univariate Cox regression result of candidate genes. |
get_Entrez_ID |
Convert gene symbol to Entrez_Gene_ID |
get_final_signature |
Identify the candidate prognosis-related pathways |
get_km_survival_curve |
Plot Kaplan-Meier survival curve. |
get_MultivariateCox_result |
Perform the multivariate Cox regression |
get_mut_status |
Converts MAF file into mutation matrix |
get_Oncoplots |
draw an GenePathwayOncoplots |
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 |
maffile |
maffile |
maf_data |
maf_data |
mut_num |
mut_num |
mut_sam |
mut_sam |
mut_sample |
mut_sample |
mut_status |
mut_status |
newspia |
newspia |
path_cox_data |
path_cox_data |
path_gene |
path_gene |
path_Ucox_mul |
path_Ucox_mul |
path_Ucox_mul_res |
path_Ucox_mul_res |
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 |