API for caravagnalab/CNAqc
CNAqc - Copy Number Analysis quality check
| Global functions | |
|---|---|
| %>% | Man page |
| .onLoad | Source code |
| Bayes_test_fragmentation | Source code |
| CCF | Man page Source code |
| CNA | Man page Source code |
| CNA_gene | Man page Source code |
| CNAqc | Man page |
| CNAqc-package | Man page |
| Mutations | Man page Source code |
| SBS | Man page Source code |
| SBS_counts | Man page |
| Sequenza_CNAqc | Man page Source code |
| absolute_to_relative_coordinates | Source code |
| add_breakpoints_to_plot | Source code |
| add_drivers_to_segment_plot | Source code |
| add_segments_to_plot | Source code |
| add_shadow_to_plot | Source code |
| add_shadow_to_plot_QC | Source code |
| add_subclonal_segments_to_plot | Source code |
| advanced_phasing | Source code |
| amplify | Source code |
| analyze_peaks | Man page Source code |
| analyze_peaks_common | Source code |
| analyze_peaks_general | Source code |
| analyze_peaks_subclonal | Source code |
| annotate_drivers_to_histogram | Source code |
| annotate_phased_drivers | Source code |
| annotate_variants | Man page Source code |
| annotate_variants_preprocess | Source code |
| as_karyotype | Source code |
| as_maftools_cohort | Man page Source code |
| as_maftools_obj | Man page Source code |
| as_ploidy | Source code |
| ascat | Source code |
| augment_with_maf | Man page Source code |
| augment_with_vep | Man page Source code |
| auto_tolerance | Man page Source code |
| auto_tune_epsilon | Source code |
| aux_plot_cohort_CNA | Source code |
| aux_plot_cohort_CNA_circular | Source code |
| bar_print_console | Source code |
| bar_print_console_scl | Source code |
| binomial_density | Source code |
| binomial_quantile_ranges | Source code |
| blank_genome | Source code |
| branching_evolution | Source code |
| ccf_adjustment_fun | Source code |
| check_custom_reference | Source code |
| chr_coordinates_GRCh38 | Man page |
| chr_coordinates_hg19 | Man page |
| combined_peak_detector | Source code |
| compute_CCF | Man page Source code |
| compute_QC_table | Source code |
| compute_delta_purity | Source code |
| compute_jumps_segments | Source code |
| delete | Source code |
| delta_vaf_karyo | Source code |
| detect_arm_overfragmentation | Man page Source code |
| detect_wg_overfragmentation | Source code |
| enforce_numeric | Source code |
| entropy_profile_2_class | Source code |
| eplot | Source code |
| evolve | Source code |
| example_PCAWG | Man page |
| example_dataset_CNAqc | Man page |
| expand_reference_chr_to_arms | Source code |
| expectations_generalised | Source code |
| expectations_subclonal | Source code |
| expected_vaf_fun | Source code |
| expected_vaf_peak | Source code |
| filter_proposals | Source code |
| fortify_CNA_segments | Source code |
| fortify_mutation_calls | Source code |
| fpr_test | Man page |
| frequentist_test_fragmentation | Source code |
| gene_coordinates_GRCh38 | Man page |
| gene_coordinates_hg19 | Man page |
| genome_double | Source code |
| get_PASS_percentage | Man page Source code |
| get_alleles | Source code |
| get_drivers | Man page Source code |
| get_karyotypes_colors | Source code |
| get_mutations | Source code |
| get_peaks | Source code |
| get_prevalent_karyotype | Source code |
| get_proposals | Source code |
| get_reference | Source code |
| has_MAF_annotations | Source code |
| has_driver_data | Source code |
| has_drivers | Source code |
| init | Man page Source code |
| initial_state | Source code |
| inspect_segment | Man page Source code |
| intogen_drivers | Man page |
| linear_evolution | Source code |
| map_mutations_to_clonal_segments | Source code |
| map_mutations_to_subclonal_segments | Source code |
| mixture_peak_detector | Source code |
| multiplicities | Source code |
| mutation | Source code |
| mutmult_single_copy | Source code |
| mutmult_two_copies_entropy | Source code |
| mutmult_two_copies_rough | Source code |
| my_ggplot_theme | Source code |
| new_mutation | Source code |
| overlap_bands | Source code |
| parse_Battenberg | Man page Source code |
| peak_detector | Source code |
| peak_detector_closest_hit_match | Source code |
| phase_to_density | Source code |
| plot.cnaqc | Man page Source code |
| plot_CCF | Man page Source code |
| plot_CCF_data | Source code |
| plot_CCF_strip | Source code |
| plot_SBS | Man page |
| plot_arm_fragmentation | Man page Source code |
| plot_data_histogram | Man page Source code |
| plot_gw_ccf | Man page Source code |
| plot_gw_counts | Man page Source code |
| plot_gw_depth | Man page Source code |
| plot_gw_vaf | Man page Source code |
| plot_icon_CNA | Man page Source code |
| plot_karyotypes | Man page Source code |
| plot_multisample_CNA | Man page Source code |
| plot_multisample_drivers | Source code |
| plot_mutation_multiplicity_entropy | Source code |
| plot_peaks_analysis | Man page Source code |
| plot_peaks_fit | Source code |
| plot_qc | Man page Source code |
| plot_segment_size_distribution | Man page Source code |
| plot_segments | Man page Source code |
| plot_segments_circular | Source code |
| plot_smoothing | Man page Source code |
| prepare_input_data | Source code |
| print.cnaqc | Man page Source code |
| purity_estimation_fun | Source code |
| purity_from_vaf | Source code |
| relative_to_absolute_coordinates | Source code |
| sequenza_fit_runner | Source code |
| simple_peak_detector | Source code |
| smooth_data | Source code |
| smooth_segments | Man page Source code |
| split_by_chromosome | Man page Source code |
| split_cna_to_arms | Source code |
| subsample | Man page Source code |
| subset_by_minimum_CCF | Man page Source code |
| subset_by_segment_karyotype | Man page Source code |
| subset_by_segment_minmutations | Man page Source code |
| subset_by_segment_totalcn | Man page Source code |
| subset_snvs | Man page Source code |
| vaf_from_ccf | Source code |
| wt_mutant_alleles | Man page Source code |
