API for parklab/SigMA
Signature Multivariate Analysis
| Global functions | |
|---|---|
| .convert_seq_to_vector | Source code |
| .flip_base | Source code |
| .flip_strand | Source code |
| .make_matrix_from_custom_list | Source code |
| .make_matrix_from_maf_list | Source code |
| .make_matrix_from_vcf_list | Source code |
| .make_type | Source code |
| .make_vector_from_custom | Source code |
| .make_vector_from_gr | Source code |
| .make_vector_from_maf | Source code |
| .make_vector_from_vcf | Source code |
| add_gbm_model | Source code |
| adjust_cutoff | Source code |
| adjust_ids | Source code |
| adjust_snvs | Source code |
| assignment | Man page Source code |
| calc_cos | Source code |
| calc_llh | Man page Source code |
| calculate_mh | Source code |
| combine_SBS_indel | Source code |
| conv_snv_matrix_to_df | Source code |
| cosine | Man page Source code |
| decompose | Man page Source code |
| determine_scale | Source code |
| find_data_setting | Source code |
| get_Sig3_llh_from_wgs_data | Source code |
| get_base_matrix | Source code |
| get_catalog | Source code |
| get_exps_mmrd | Source code |
| get_inter_tt_suppl | Source code |
| get_sig_exps | Source code |
| get_threshold | Source code |
| get_trinuc_counts | Source code |
| get_trinuc_norm | Source code |
| get_tumor_types_for_signature | Source code |
| get_wgs_data_for_llh | Source code |
| has_model | Source code |
| info_stat | Source code |
| list_data_options | Source code |
| list_tumor_types | Source code |
| lite_df | Man page Source code |
| llh_max_characteristics | Source code |
| llh_max_characteristics_wgs_data | Source code |
| make_matrix | Man page Source code |
| match_to_catalog | Man page Source code |
| mh_from_vcf | Source code |
| mmej_nhej_indels_from_vcfs | Source code |
| overlap_repeats | Source code |
| plot_detailed | Man page Source code |
| plot_summary | Man page Source code |
| plot_tribase_dist | Man page Source code |
| predict_mmrd | Source code |
| predict_mva | Man page Source code |
| predict_prob | Source code |
| quick_simulation | Source code |
| remove_gbm_model | Source code |
| run | Man page Source code |
| run_overlap_repeats | Source code |
| sen_fpr | Source code |
| simulate_from_wgs | Source code |
| subsample | Source code |
| subsample_id | Source code |
| tune_gbm_model | Source code |
| tune_new_gbm | Source code |
