NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(.DollarNames,CESAnalysis)
S3method(.DollarNames,CompoundVariantSet)
export(CESAnalysis)
export(CompoundVariantSet)
export(add_covered_regions)
export(add_variants)
export(annotate_variants)
export(assign_group_average_trinuc_rates)
export(baseline_mutation_rates)
export(build_RefCDS)
export(ces_epistasis)
export(ces_gene_epistasis)
export(ces_variant)
export(check_sample_overlap)
export(create_refset)
export(define_compound_variants)
export(epistasis_results)
export(excluded_maf_records)
export(gene_mutation_rates)
export(get_ces_signature_set)
export(get_gene_rates)
export(get_sample_info)
export(get_signature_weights)
export(get_trinuc_rates)
export(list_ces_covariates)
export(list_ces_refsets)
export(list_ces_signature_sets)
export(load_cesa)
export(load_maf)
export(lollipops)
export(maf_records)
export(pairwise_epistasis_lik)
export(preload_maf)
export(save_cesa)
export(select_variants)
export(set_gene_rates)
export(set_refset_dir)
export(set_signature_weights)
export(set_trinuc_rates)
export(snv_results)
export(sswm_lik)
export(sswm_sequential_lik)
export(suggest_cosmic_signatures_to_remove)
export(trinuc_mutation_rates)
export(validate_signature_set)
import(BSgenome)
import(GenomeInfoDb)
import(data.table)
import(ggplot2)
import(ggrepel)