Pathway Based Tumor Mutational Burden

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Documentation for package ‘pathwayTMB’ version 0.1.3

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

Help Pages

final_character	final_character, the example's final signature
GenePathwayOncoplots	draw an GenePathwayOncoplots
genesmbol	genesmbol, the coding genes' length
gene_path	gene_path, the pathways geneset
get_final_signature	Filter cancer-specific dysfunction pathways.
get_mut_matrix	Converts MAF into mutation matrix.
get_PTMB	Calculate the Pathway-based Tumor Mutational Burden.
mut_matrix	mut_matrix, mutations matrix
plotKMcurves	Drawing Kaplan Meier Survival Curves Using the final survival-related PTMB.
plotMutInteract	Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways.
plotROC	plot the ROC curve
PTMB_matrix	PTMB_matrix, the Pathway-based Tumor Mutational Burden matrix
sur	sur, the samples' survival data