A Driver Discovery Tool for Cancer Whole Genomes

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Documentation for package ‘ActiveDriverWGS’ version 1.2.0

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.fix_all_results fix_all_results verifies that the results table has the correct format and p-values
.get_3n_context_of_mutations This function finds the tri-nucleotide context of mutations
.get_obs_exp Calculates the number of expected mutations based
.get_signf_results Returns significant results
.make_mut_signatures Makes mutational signatures
.split_coord_fragments_in_BED Splits a BED12 file into separate regions
ActiveDriverWGS ActiveDriverWGS is a driver discovery tool for simple somatic mutations in cancer whole genomes
ADWGS_test ADWGS_test executes the statistical test for ActiveDriverWGS
cancer_genes cancer_genes
cancer_gene_sites post-translational modification sites found in cancer genes
cll_mutations CLL mutations
format_muts This function filters hypermutated samples and returns the formatted mutations with the appropriate trinucleotide context
prepare_elements_from_BED12 Prepares element coords from a BED12 file
prepare_elements_from_BED4 Prepares element coords from a BED4 file