Function reference • HPOExplorer

All functions
`add_ancestor()` `add_death()` `add_disease()` `add_disease_genes()` `add_evidence()` `add_gene_frequency()` `add_genes()` `add_gpt_annotations()` `add_hpo_definition()` `add_hpo_id()` `add_hpo_name()` `add_info_content()` `add_mondo()` `add_ndisease()` `add_omop()` `add_onset()` `add_ont_lvl()` `add_pheno_frequency()` `add_prevalence()` `add_severity()` `add_tier()`	Add functions
`disease_id_to_omop`	Human Phenotype Ontology: Disease ID to OMOP
`filter_descendants()`	Filter functions
`get_hpo()` `get_hpo_id_direct()`	Get functions
`get_gene_lists()`	Get gene list
`get_top_phenos()`	Get top phenotypes
`gpt_annot_check()`	Check annotations from GPT
`gpt_annot_class()`	GPT annotations: add severity class
`gpt_annot_codify()`	Check annotations from GPT
`gpt_annot_melt()`	Melt annotations from GPT
`gpt_annot_plot()`	Plot annotations from GPT
`gpt_annot_plot_branches()`	Plot annotations from GPT: by branch
`gpt_annot_read()`	Read annotations from GPT
`hpo_api()`	HPO API
`hpo_deaths`	Human Phenotype Ontology: Age of Death
`hpo_frequencies`	Human Phenotype Ontology: phenotype frequencies
`hpo_id_to_omop`	Human Phenotype Ontology: HPO ID to OMOP
`hpo_modifiers`	Human Phenotype Ontology: disease modifiers
`hpo_onsets`	Human Phenotype Ontology: disease onset
`hpo_tiers`	Human Phenotype Ontology: disease severity tiers
`hpo_tiers_auto`	Human Phenotype Ontology: disease severity tiers (auto)
`hpo_to_matrix()`	HPO to matrix
`list_columns()`	List columns
`load_phenotype_to_genes()`	Load phenotype_to_genes
`annotate_phenos()` `example_phenos()`	Main functions
`make_igraph_object()` `make_network_object()` `make_network_plot()` `make_phenos_dataframe()` `make_tiers()`	Make functions
`list_deaths()` `list_onsets()`	Map functions
`map_phenotypes()`	Harmonise phenotypes
`newlines_to_definition()`	Add new lines to disease description
`per_branch_plot()`	Plot N phenotypes per branch
`phenos_to_granges()`	Phenotypes to GenomicRanges
`plot_evidence()`	Plot evidence
`plot_top_phenos()`	Plot top phenotypes
`search_hpo()`	Search the Human Phenotype Ontology

Reference

All functions