API for lm687/CompSign
Study of mutational signatures using compositional data analysis (CoDA) techniques
| Global functions | |
|---|---|
| .onLoad | Source code |
| L_to_cov | Source code |
| L_to_cov_wrapper_TMB | Man page Source code |
| QPsig | Source code |
| TMBobj_partialILR_remove_single_obs | Source code |
| adjust_all | Source code |
| clean_name | Source code |
| clean_name_fullRE | Source code |
| clean_name_fullRE_2 | Source code |
| compare_betas_tmb | Source code |
| compare_signaturefit_to_data | Source code |
| comparison_betas_models | Source code |
| comparison_betas_models2 | Source code |
| comparison_randomintercepts_models | Source code |
| createBarplot | Man page Source code |
| createbarplot_object | Source code |
| extract_sigs | Source code |
| extract_sigs_TMB_obj | Source code |
| fill_covariance_matrix | Source code |
| get_count_object | Source code |
| get_count_object_file | Source code |
| give_UNSTRUCTURED_CORR_t_matrix | Source code |
| give_all_correlations | Source code |
| give_amalgamated_exposures | Source code |
| give_amalgamated_exposures_TMBobj | Source code |
| give_amalgamation | Source code |
| give_barplot | Source code |
| give_barplot_from_obj | Source code |
| give_betas | Source code |
| give_confidence_interval | Source code |
| give_dummy_colnames | Source code |
| give_dummy_rownames | Source code |
| give_first_col | Source code |
| give_ggplot_sig_cor_TMB | Source code |
| give_interval_plots | Source code |
| give_interval_plots_2 | Source code |
| give_length_cov | Source code |
| give_min_pert | Source code |
| give_pairs_with_mvn | Source code |
| give_pairs_with_mvn_wrapper | Source code |
| give_params_in_CI | Source code |
| give_perturbation_TMBobj | Source code |
| give_plot_fits_wrapper | Source code |
| give_ranked_plot_simulation | Source code |
| give_sim_from_estimates | Source code |
| give_stderr | Source code |
| give_subset_samples_TMBobj | Source code |
| give_subset_samples_TMBobj_2 | Source code |
| give_subset_sigs | Source code |
| give_subset_sigs_TMBobj | Source code |
| give_summary_of_runs2 | Source code |
| give_summary_per_sample | Source code |
| give_ternary | Source code |
| give_ternary_v2 | Source code |
| give_totalperturbation_TMBobj | Source code |
| give_totalperturbation_TMBobj_sigaverage | Source code |
| give_weightedtotalperturbation_TMBobj | Source code |
| give_x_matrix | Man page Source code |
| give_z_matrix | Man page Source code |
| is_slope | Source code |
| load_PCAWG | Man page Source code |
| load_models | Source code |
| make.names_allowing_hyphen | Source code |
| modify_dataset | Man page Source code |
| nan_to_zero | Source code |
| non_duplicated_rows | Source code |
| normalise_cl | Source code |
| normalise_rw | Source code |
| object_to_cov_heatmap | Source code |
| plot_betas | Source code |
| plot_betas_minimal_perturbation | Source code |
| plot_estimates_TMB | Source code |
| plot_lambdas | Source code |
| plot_ternary | Source code |
| python_like_select | Source code |
| python_like_select_colnames | Source code |
| python_like_select_name | Source code |
| python_like_select_rownames | Source code |
| re_vector_to_matrix | Source code |
| reflect_matrix | Source code |
| remove_all_NA | Source code |
| remove_na | Source code |
| rename_Y_dollar | Source code |
| resort_columns | Source code |
| rm_na_rows | Source code |
| select_intercept | Source code |
| select_self | Source code |
| select_slope_2 | Source code |
| simulate_from_DMSL_TMB | Source code |
| simulate_from_DM_TMB | Source code Source code |
| simulate_from_M_TMB | Source code Source code |
| simulate_from_correlated_binom | Source code |
| softmax | Man page Source code |
| sort_columns_TMB | Source code |
| sort_columns_TMB_SBS1 | Source code |
| split_matrix_in_half | Source code |
| split_rows | Source code |
| summarise_DA_detection | Source code |
| ttest_TMB_wrapper_overdisp | Source code |
| vector_cats_to_logR | Source code |
| vector_to_ct_list | Man page Source code |
| wald_TMB_wrapper | Man page Source code |
| wald_TMB_wrapper_overdisp | Source code |
| wald_generalised | Source code |
| wrapper_run_HMP_Xdc.sevsample | Source code |
| wrapper_run_HMP_Xmcupo.sevsample | Source code |
| wrapper_run_TMB | Man page Source code |
| wrapper_run_ttest_ilr | Source code |
| wrapper_run_ttest_props | Source code |
