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 |