# Identify Prognosis-Related Pathways Altered by Somatic Mutation

## Documentation for package ‘PMAPscore’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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