hpo_deaths: Human Phenotype Ontology: Age of Death

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

Human Phenotype Ontology: Age of Death

Description

Age of Death associated with each disease, and by extension, each phenotype.

Usage

data("hpo_deaths")

Format

data.table

Source

terms <- simona::dag_offspring(get_hpo(), term = "HP:0011420") aod <- lapply(stats::setNames(terms, terms), function(hpo_id){ message("Extracting API data for",hpo_id) d <- hpo_api(hpo_id = hpo_id, type = "diseases")$diseases }) |> data.table::rbindlist(fill = TRUE, use.names = TRUE, idcol = "AgeOfDeath") aod$AgeOfDeath_name <- map_phenotypes(terms = aod$AgeOfDeath) #### Convert AoD to numeric scores #### dict <- HPOExplorer:::hpo_dict(type="AgeOfDeath") aod$AgeOfDeath_score <- dict[aod$AgeOfDeath_name] data.table::setnames(aod, c("diseaseId","diseaseName"), c("disease_id","disease_name")) hpo_deaths <- aod usethis::use_data(hpo_deaths, overwrite = TRUE)

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