Get functions

Source: R/0docs.R, R/get_hpo.R, R/get_hpo_id_direct.R

Functions to get data objects and extract elements.

get_hpo(
  lvl,
  add_ancestors = 2,
  force_new = FALSE,
  terms = NULL,
  method = "github",
  save_dir = KGExplorer::cache_dir(package = "HPOExplorer"),
  ...
)

get_hpo_id_direct(term, hpo = get_hpo())

Arguments

lvl

How many levels deep into the ontology to get ancestors from. For example:

  • 1: "All"

  • 2: "Phenotypic abnormality"

  • 3: "Abnormality of the nervous system"

  • 4: "Abnormality of nervous system physiology"

  • 5: "Neurodevelopmental abnormality" or "Behavioral abnormality"

add_ancestors

Add ancestors for each term.

force_new

Force a new download or creation of a data resource.

terms

A subset of HPO IDs to assign Tiers to.

method

Method to construct plot with.

save_dir

Directory to save a file to.

...

Arguments passed on to KGExplorer::get_ontology

name
filetype

File type to search for.

add_metadata

Add metadata to the resulting ontology object.

add_n_edges

Add the number of edges (connections) for each term.

add_ontology_levels

Add the ontology level for each term.

term

One or more ontology IDs.

hpo

Human Phenotype Ontology object, loaded from get_ontology.

Value

Data.

ontology_DAG object.

The HPO ID(s) of phenotype(s)

Functions

  • get_hpo(): get_ Get Human Phenotype Ontology (HPO)

    Updated version of Human Phenotype Ontology (HPO). Created from the OBO files distributed by the HPO project's GitHub.

    By comparison, the hpo data from ontologyIndex is from 2016. Note that the maximum ontology level depth in the 2016 version was 14, whereas in the 2023 version the maximum ontology level depth is 16 (due to an expansion of the HPO).

  • get_hpo_id_direct(): get_ Get HPO term ID direct

    Directly retrieves it from the HPO ontology object.

Examples

hpo <- get_hpo()
term = "Phenotypic abnormality"
pheno_abnormality_id <- get_hpo_id_direct(term = term)