Identify Prognosis-Related Pathways Altered by Somatic Mutation
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Documentation for package ‘PMAPscore’ version 0.1.1
Help Pages
| 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 |