add_disease: Add diseases

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

Add diseases

Description

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

Usage

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)

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