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: 326
#> - physical_malformations: 81
#> - blindness: 1
#> - sensory_impairments: 253
#> - immunodeficiency: 29
#> - cancer: 56
#> - reduced_fertility: 9