Man pages for GeneAccord
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
| all_genes_tbl | Different gene id's and their chromosomal location. |
| avg_rates_m | The average rates of clonal exclusivity of the example data... |
| build_null_test_statistic | Simulate pairs to generate values of the test statistic under... |
| clone_tbl_all_pats_all_trees | The tibble with gene-to-clone assignments from all patients... |
| compute_rates_clon_excl | Get rates of clonal exclusivity for each tree inference |
| compute_test_stat_avg_rate | Compute the test statistic of the clonal exclusivity test... |
| convert_ensembl_to_reactome_pw_tbl | Map ensembl gene id clone tibble to reactome pathway clone... |
| create_ensembl_gene_tbl_hg | Get a tibble of all gene ensembl id's, gene names (hgnc),... |
| create_tbl_ent_clones | Get clone alteration tibble. |
| create_tbl_tree_collection | Get clone alteration tibble across the collection of trees. |
| ecdf_list | The list with the ECDF's of the test statistic under the null... |
| ecdf_lr_test_clon_excl_avg_rate | Compare observed likelihood ratio test statistic to its ecdf... |
| ensembl_to_hgnc | Get the hgnc gene symbol for an ensembl gene id. |
| ensembl_to_reactome | Get the reactome pathways for an ensembl gene id. |
| ensg_reactome_path_map | Ensembl gene id's and the Reactome pathways. |
| ensmusg_reactome_path_map | Ensembl gene id's and the Reactome pathways - for mouse! |
| extract_num_clones_tbl | Extract number of clones. |
| GeneAccord | Detection of clonally exclusive gene or pathway pairs in a... |
| generate_ecdf_test_stat | Generate the ECDF of the test statistic under the null... |
| generate_test_stat_hist | Generate the test statistic and p-values under the null... |
| get_hist_clon_excl | Compute all values of how often gene pairs were clonally... |
| get_hist_clon_excl_this_pat_this_pair | Check for a pair how often it was mutated in the current... |
| get_rate_diff_branch_ent_pair | Compute rate of being in different branches/clones. |
| heatmap_clones_gene_pat | Heatmaps of gene pairs of interest |
| hgnc_to_ensembl | Get the ensembl gene id for a hgnc gene symbol. |
| is_diff_branch_ent_pair | Check whether pair is in different branches/clones. |
| list_of_clon_excl_all_pats | The list with the histogram of how often pairs are clonally... |
| list_of_num_trees_all_pats | The list with the histogram of how often pairs are occurring... |
| map_pairs_to_hgnc_symbols | Map the ensembl gene ids to hgnc symbols from a tibble |
| merge_clones_identical_ents | Merge identical entities in clone tibble from one patient |
| pairs_in_patients_hist | Pairs in how many patients histogram |
| plot_ecdf_test_stat | Plot empirical cumulative distribution functions of the test... |
| plot_rates_clon_excl | Barplot of rates of clonal exclusivity and number of clones. |
| take_pairs_and_get_patients | Get the patients in which pairs are mutated |
| vis_pval_distr_num_pat | Plot histogram and empirical cumulative distribution function... |
| write_res_pairs_to_disk | Write resulting significant pairs to disk |
