search_hpo: Search the Human Phenotype Ontology

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Search the Human Phenotype Ontology

Description

Serarch for phenotypes in the HPO that match substring queries, or are the descendants of those substring-matched phenotypes.

Usage

search_hpo(
  hpo = get_hpo(),
  queries = list(intellectual_disability = c("Intellectual disability",
    "Mental deterioration"), impaired_mobility = c("Gait disturbance",
    "Diminished movement", " mobility"), physical_malformations = c("malformation"),
    blindness = c("^blindness"), sensory_impairments = c("Abnormality of vision",
    "Abnormality of the sense of smell", "Abnormality of taste sensation",
    "Somatic sensory dysfunction", "Hearing abnormality"), immunodeficiency =
    c("Immunodeficiency", "Impaired antigen-specific response"), cancer = c("Cancer", 
  
      "malignant", "carcinoma"), reduced_fertility = c("Decreased fertility",
    "Hypogonadism")),
  search_cols = c("name"),
  include_descendants = TRUE,
  include_ancestors = FALSE,
  ignore.case = TRUE,
  fixed = FALSE,
  verbose = TRUE
)

Arguments

hpo	Human Phenotype Ontology object, loaded from get_ontology.
queries	A named list of character vectors. Each vector includes a phenoptype name (or a substring) to be searched for in the HPO.
search_cols	HPO metadata column names to query for hits.
include_descendants	Include all descendants of query hits.
include_ancestors	Include all ancestors of query hits.
ignore.case	if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching.
fixed	logical. If TRUE, pattern is a string to be matched as is. Overrides all conflicting arguments.
verbose	Print messages.

Value

Named list of HPO IDs.

Examples

query_hits <- search_hpo()

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.