Add diseases

Annotate each HPO term with diseases that they are associated with.

add_disease(
  phenos,
  phenotype_to_genes = load_phenotype_to_genes(),
  hpo = get_hpo(),
  add_descriptions = FALSE,
  all.x = TRUE,
  use_api = FALSE,
  workers = NULL,
  allow.cartesian = FALSE
)

Arguments

phenos

A data.table containing HPO IDs and other metadata.

phenotype_to_genes

Output of load_phenotype_to_genes mapping phenotypes to gene annotations.

hpo

Human Phenotype Ontology object, loaded from get_ontology.

add_descriptions

Add disease names and descriptions.

all.x

logical; if TRUE, rows from x which have no matching row in y are included. These rows will have 'NA's in the columns that are usually filled with values from y. The default is FALSE so that only rows with data from both x and y are included in the output.

use_api

Get definitions from the HPO API, as opposed to a static local dataset.

workers

Number (>1) or proportion (<1) of worker cores to use.

allow.cartesian

See allow.cartesian in [.data.table.

Examples

phenos <- example_phenos()
phenos2 <- add_disease(phenos = phenos)
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> Adding genes and disease IDs.