Serarch for phenotypes in the HPO that match substring queries, or are the descendants of those substring-matched phenotypes.
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
)Human Phenotype Ontology object, loaded from get_ontology.
A named list of character vectors. Each vector includes a phenoptype name (or a substring) to be searched for in the HPO.
HPO metadata column names to query for hits.
Include all descendants of query hits.
Include all ancestors of query hits.
if FALSE, the pattern matching is case
sensitive and if TRUE, case is ignored during matching.
logical. If TRUE, pattern is a string to be
matched as is. Overrides all conflicting arguments.
Print messages.
Named list of HPO IDs.
query_hits <- search_hpo()
#> Querying HPO for matching terms.
#> Number of phenotype hits per query group:
#> - intellectual_disability: 19
#> - impaired_mobility: 322
#> - physical_malformations: 81
#> - blindness: 1
#> - sensory_impairments: 252
#> - immunodeficiency: 29
#> - cancer: 56
#> - reduced_fertility: 9