Man pages for Townsend-Lab-Yale/cancereffectsizeR
Calculate Cancer Effect Size
| aac_to_snv_ids | Get SNVs that cause an amino acid change |
| add_covered_regions | add_covered_regions |
| add_variants | Add variant annotations |
| annotate_variants | Annotate variants |
| artifact_account | Calculate relative rates of biological mutational processes |
| assign_group_average_trinuc_rates | Skip mutational signature analysis and assign group average... |
| assign_gr_to_coverage | assign_gr_to_coverage |
| baseline_mutation_rates | Baseline mutation rate calculation |
| build_RefCDS | cancereffectsizeR's RefCDS builder |
| calculate_trinuc_rates | Calculate trinuc rates |
| CESAnalysis | Create a cancereffectsizeR analysis |
| ces_epistasis | Variant-level pairwise epistasis |
| ces_gene_epistasis | Gene-level epistasis |
| ces_variant | Calculate cancer effects of variants |
| check_for_ref_data | check_for_ref_data |
| check_sample_overlap | Catch duplicate samples |
| clean_granges_for_cesa | clean_granges_for_cesa |
| clear_effect_output | Clear variant effect output |
| clear_epistasis_output | Clear epistasis output |
| clear_gene_rates | Clear regional mutation rates |
| clear_sample_data | Clear sample data |
| clear_trinuc_rates_and_signatures | Clear mutational signature attributions and related mutation... |
| complete_aac_ids | Create full AAC ID |
| CompoundVariantSet | Create CompoundVariantSet from variant IDs |
| convert_signature_weights_for_mp | Get MutationalPatterns contributions matrix |
| copy_cesa | Create an independent copy of a CESAnalysis |
| cosmic_signature_info | Get COSMIC signature descriptions |
| create_refset | Create a custom refset |
| define_compound_variants | Divide batches of variants into a CompoundVariantSet |
| detect_mnv | Find likely MNVs in an MAF table |
| dot-add_covered_regions | .add_covered_regions |
| dot-variant_counts | Internal variant prevalence and coverage calculation |
| epistasis_results | View output from epistasis functions |
| excluded_maf_records | View excluded MAF data |
| gene_mutation_rates | Use dNdScv with tissue-specific covariates to calculate... |
| get_cesa_bsg | get_cesa_bsg |
| get_ces_signature_set | get_ces_signature_set |
| get_dndscv_model_fit | This little function called by gene_mutation_rates() is... |
| get_gene_rates | Get table of neutral gene mutation rates |
| get_gr_from_table | Get GRanges from chr/start/end table |
| get_PathScore_coding_regions | Get PathScore coding regions |
| get_ref_data | get_ref_data |
| get_refset_dirs | get_refset_dirs |
| get_sample_info | View sample metadata |
| get_signature_weights | Get table of signature attributions |
| get_TCGA_project_MAF | Get MAF data from TCGA cohort |
| get_trinuc_rates | Get estimated relative rates of trinucleotide-specific SNV... |
| identify_maf_variants | Annotate MAF data with variant types and variant IDs |
| list_ces_covariates | list_ces_covariates |
| list_ces_refsets | list_ces_refsets |
| list_ces_signature_sets | list_ces_signature_sets |
| load_cesa | Load a previously saved CESAnalysis |
| load_maf | Load MAF somatic mutation data |
| load_sample_data | Add sample data |
| maf_records | View data loaded into CESAnalysis |
| make_PathScore_input | Make a PathScore input file from MAF data |
| mutational_signature_effects | Attribute cancer effects to mutational signatures |
| pairwise_epistasis_lik | pairwise_epistasis_lik |
| pairwise_variant_epistasis | Calculate SIs at variant level under pairwise epistasis model |
| plot_effects | Plot cancer effects |
| plot_signature_effects | Plot mutational source and effect attributions |
| preload_maf | Read and verify MAF somatic mutation data |
| preload_ref_data | preload_ref_data |
| read_in_maf | Load MAF somatic mutation data |
| read_vcf | Internal VCF parser |
| run_deconstructSigs | cancereffectsizeR wrapper for deconstructSigs |
| run_dndscv | Internal function to run dNdScv |
| run_mutational_patterns | cancereffectsizeR wrapper for fit_to_signatures |
| samples_with | Find samples with specified variants |
| save_cesa | Save a CESAnalysis in progress |
| select_samples | Retrieve validated subset of CESAnalysis samples table |
| select_variants | Select and filter variants |
| set_gene_rates | Assign pre-calculated regional mutation rates |
| set_refset_dir | Set reference data directory |
| set_signature_weights | Set SNV signature weights |
| set_trinuc_rates | Assign pre-calculated relative trinucleotide mutation rates |
| snv_results | View results from ces_variant |
| sort_and_validate_variant_ids | Sort and validate input variant IDs |
| sswm_lik | sswm_lik |
| suggest_cosmic_signature_exclusions | Tissue-specific mutational signature exclusions |
| trinuc_mutation_rates | Calculate relative rates of trinucleotide-context-specific... |
| trinuc_snv_counts | Tabulate SNVs by trinucleotide context |
| univariate_si_conf_ints | Calculate uniroot CIs on selection intensities |
| update_covered_in | update_covered_in |
| validate_aac_ids | Ensure AAC IDs are valid for a given reference data set |
| validate_signature_set | validate_signature_set |
| validate_snv_ids | validate_snv_ids |
| variant_counts | Assess variant prevalence and coverage |
| vcfs_to_maf_table | Read a VCF into an MAF-like table |
