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PMAPscore (version 0.1.1)

Identify Prognosis-Related Pathways Altered by Somatic Mutation

Description

We innovatively defined a pathway mutation accumulate perturbation score (PMAPscore) to reflect the position and the cumulative effect of the genetic mutations at the pathway level. Based on the PMAPscore of pathways, identified prognosis-related pathways altered by somatic mutation and predict immunotherapy efficacy by constructing a multiple-pathway-based risk model (Tarca, Adi Laurentiu et al (2008) ).

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Version

Install

install.packages('PMAPscore')

Monthly Downloads

212

Version

0.1.1

License

GPL (>= 2)

Maintainer

Junwei Han

Last Published

April 12th, 2022

Functions in PMAPscore (0.1.1)

Converts MAF file into mutation matrix

get_response_plot

Plot the response column diagram

Calculates the pathway-based mutation accumulate perturbation score

get_univarCox_result

Perform the univariate Cox regression analysis.

path_Ucox_mul_res

path_Ucox_mul_res

roc_data, the data frame use for ploting ROC curve

Calculates the risk score for patients

Plot the ROC curve

get_km_survival_curve

Plot Kaplan-Meier survival curve.

final_signature

final_signature, the final prognosis-related pathways

Convert gene symbol to Entrez_Gene_ID

get_final_signature

Identify the candidate prognosis-related pathways

draw an GenePathwayOncoplots

gene_symbol_Entrez

gene_symbol_Entrez, the genes' symbol and ENTREZID

gene_Ucox_res, the univariate Cox regression result of candidate genes.

get_MultivariateCox_result

Perform the multivariate Cox regression