# Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

## Documentation for package ‘GeneAccord’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

all_genes_tbl | Different gene id's and their chromosomal location.
avg_rates_m | The average rates of clonal exclusivity of the example data set used in the vignette
build_null_test_statistic | Simulate pairs to generate values of the test statistic under the null distribution
clone_tbl_all_pats_all_trees | The tibble with gene-to-clone assignments from all patients and all trees
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 (lrtest).
convert_ensembl_to_reactome_pw_tbl | Map ensembl gene id clone tibble to reactome pathway clone tibble.
create_ensembl_gene_tbl_hg | Get a tibble of all gene ensembl id's, gene names (hgnc), entrez gene id's, uniprot/swissprot gene id's and genomic coordinates.
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 hypothesis
ecdf_lr_test_clon_excl_avg_rate | Compare observed likelihood ratio test statistic to its ecdf under null.
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 cohort of cancer patients
generate_ecdf_test_stat | Generate the ECDF of the test statistic under the null distribution - taking the average rates of clonal exclusivity
generate_test_stat_hist | Generate the test statistic and p-values under the null distribution
get_hist_clon_excl | Compute all values of how often gene pairs were clonally exclusive across all trees for a patient.
get_hist_clon_excl_this_pat_this_pair | Check for a pair how often it was mutated in the current patient across trees, and how often also clonally exclusive.
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 exclusive across the collection of trees
list_of_num_trees_all_pats | The list with the histogram of how often pairs are occurring across the collection of trees
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 statistic under the null.
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 of p-values.
write_res_pairs_to_disk | Write resulting significant pairs to disk