API for Townsend-Lab-Yale/cancereffectsizeR
Calculate Cancer Effect Size
| Global functions | |
|---|---|
| .DollarNames.CESAnalysis | Source code |
| .add_covered_regions | Man page Source code |
| .variant_counts | Man page |
| CESAnalysis | Man page Source code |
| CompoundVariantSet | Man page Source code |
| aac_to_snv_ids | Man page Source code |
| add_covered_regions | Man page Source code |
| add_variants | Man page Source code |
| annotate_variants | Man page Source code |
| artifact_account | Man page |
| assign_gr_to_coverage | Man page Source code |
| assign_group_average_trinuc_rates | Man page Source code |
| baseline_mutation_rates | Man page Source code |
| build_RefCDS | Man page Source code |
| calculate_trinuc_rates | Man page |
| ces_epistasis | Man page Source code |
| ces_gene_epistasis | Man page Source code |
| ces_variant | Man page Source code |
| check_for_ref_data | Man page Source code |
| check_sample_overlap | Man page |
| clean_granges_for_cesa | Man page |
| clear_effect_output | Man page |
| clear_epistasis_output | Man page |
| clear_gene_rates | Man page |
| clear_sample_data | Man page Source code |
| clear_trinuc_rates_and_signatures | Man page |
| complete_aac_ids | Man page Source code |
| convert_signature_weights_for_mp | Man page |
| copy_cesa | Man page Source code |
| cosmic_signature_info | Man page |
| create_refset | Man page Source code |
| define_compound_variants | Man page |
| detect_mnv | Man page Source code |
| epistasis_results | Man page |
| error | Source code |
| excluded_maf_records | Man page |
| gene_mutation_rates | Man page Source code |
| get_PathScore_coding_regions | Man page |
| get_TCGA_project_MAF | Man page Source code |
| get_ces_signature_set | Man page Source code |
| get_cesa_bsg | Man page Source code |
| get_dndscv_model_fit | Man page |
| get_gene_rates | Man page |
| get_gr_from_table | Man page |
| get_ref_data | Man page Source code |
| get_refset_dirs | Man page Source code |
| get_sample_info | Man page |
| get_signature_weights | Man page |
| get_trinuc_rates | Man page |
| identify_maf_variants | Man page |
| list_ces_covariates | Man page Source code |
| list_ces_refsets | Man page Source code |
| list_ces_signature_sets | Man page Source code |
| load_cesa | Man page Source code |
| load_maf | Man page Source code |
| load_sample_data | Man page Source code |
| maf_records | Man page |
| make_PathScore_input | Man page Source code |
| mutational_signature_effects | Man page Source code |
| pairwise_epistasis_lik | Man page Source code |
| pairwise_variant_epistasis | Man page |
| plot_effects | Man page Source code |
| plot_signature_effects | Man page Source code |
| preload_maf | Man page Source code |
| preload_ref_data | Man page Source code |
| pretty_message | Source code |
| read_in_maf | Man page Source code |
| read_vcf | Man page Source code |
| run_deconstructSigs | Man page Source code |
| run_dndscv | Man page |
| run_mutational_patterns | Man page Source code |
| samples_with | Man page Source code |
| save_cesa | Man page Source code |
| select_samples | Man page Source code |
| select_variants | Man page Source code |
| set_gene_rates | Man page Source code |
| set_refset_dir | Man page |
| set_signature_weights | Man page Source code |
| set_trinuc_rates | Man page Source code |
| snv_results | Man page |
| sort_and_validate_variant_ids | Man page |
| sswm_lik | Man page Source code |
| suggest_cosmic_signature_exclusions | Man page Source code |
| trinuc_mutation_rates | Man page Source code |
| trinuc_snv_counts | Man page |
| univariate_si_conf_ints | Man page Source code |
| update_covered_in | Man page Source code |
| validate_aac_ids | Man page Source code |
| validate_signature_set | Man page Source code |
| validate_snv_ids | Man page Source code |
| variant_counts | Man page Source code |
| vcfs_to_maf_table | Man page Source code |
| warning | Source code Source code Source code Source code Source code |
