Identify Prognosis-Related Pathways Altered by Somatic Mutation
Converts MAF file into mutation matrix
draw an GenePathwayOncoplots
Calculates the pathway-based mutation accumulate perturbation score
Plot the response column diagram
Calculates the risk score for patients
Plot the ROC curve
Convert gene symbol to Entrez_Gene_ID
Identify the candidate prognosis-related pathways
Plot Kaplan-Meier survival curve.
Perform the multivariate Cox regression
get_sam_cla
Perform the univariate Cox regression analysis.
newspia
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) <doi:10.1093/bioinformatics/btn577>).