Man pages for cbg-ethz/GeneAccord
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

all_genes_tblDifferent gene id's and their chromosomal location.
avg_rates_mThe average rates of clonal exclusivity of the example data...
build_null_test_statisticSimulate pairs to generate values of the test statistic under...
clone_tbl_all_pats_all_treesThe tibble with gene-to-clone assignments from all patients...
compute_rates_clon_exclGet rates of clonal exclusivity for each tree inference
compute_test_stat_avg_rateCompute the test statistic of the clonal exclusivity test...
convert_ensembl_to_reactome_pw_tblMap ensembl gene id clone tibble to reactome pathway clone...
create_ensembl_gene_tbl_hgGet a tibble of all gene ensembl id's, gene names (hgnc),...
create_tbl_ent_clonesGet clone alteration tibble.
create_tbl_tree_collectionGet clone alteration tibble across the collection of trees.
ecdf_listThe list with the ECDF's of the test statistic under the null...
ecdf_lr_test_clon_excl_avg_rateCompare observed likelihood ratio test statistic to its ecdf...
ensembl_to_hgncGet the hgnc gene symbol for an ensembl gene id.
ensembl_to_reactomeGet the reactome pathways for an ensembl gene id.
ensg_reactome_path_mapEnsembl gene id's and the Reactome pathways.
ensmusg_reactome_path_mapEnsembl gene id's and the Reactome pathways - for mouse!
extract_num_clones_tblExtract number of clones.
GeneAccordDetection of clonally exclusive gene or pathway pairs in a...
generate_ecdf_test_statGenerate the ECDF of the test statistic under the null...
generate_test_stat_histGenerate the test statistic and p-values under the null...
get_hist_clon_exclCompute all values of how often gene pairs were clonally...
get_hist_clon_excl_this_pat_this_pairCheck for a pair how often it was mutated in the current...
get_rate_diff_branch_ent_pairCompute rate of being in different branches/clones.
heatmap_clones_gene_patHeatmaps of gene pairs of interest
hgnc_to_ensemblGet the ensembl gene id for a hgnc gene symbol.
is_diff_branch_ent_pairCheck whether pair is in different branches/clones.
list_of_clon_excl_all_patsThe list with the histogram of how often pairs are clonally...
list_of_num_trees_all_patsThe list with the histogram of how often pairs are occurring...
map_pairs_to_hgnc_symbolsMap the ensembl gene ids to hgnc symbols from a tibble
merge_clones_identical_entsMerge identical entities in clone tibble from one patient
pairs_in_patients_histPairs in how many patients histogram
plot_ecdf_test_statPlot empirical cumulative distribution functions of the test...
plot_rates_clon_exclBarplot of rates of clonal exclusivity and number of clones.
take_pairs_and_get_patientsGet the patients in which pairs are mutated
vis_pval_distr_num_patPlot histogram and empirical cumulative distribution function...
write_res_pairs_to_diskWrite resulting significant pairs to disk
cbg-ethz/GeneAccord documentation built on Aug. 12, 2018, 12:14 a.m.