Map functions

Source: R/0docs.R, R/list_deaths.R, R/list_onsets.R

Functions to map IDs.

list_deaths(
  hpo = get_hpo(),
  exclude = FALSE,
  to = c("name", "id"),
  include_na = TRUE
)

list_onsets(
  hpo = get_hpo(),
  exclude = FALSE,
  to = c("name", "id"),
  include_na = TRUE,
  verbose = TRUE
)

Arguments

hpo

Human Phenotype Ontology object, loaded from get_ontology.

exclude

HPO phenotype names to exclude.

to

Character vector of database(s) to map IDs to. When not "mondo", can supply multiple alternative databases to map to (e.g. c("OMIM","Orphanet","DECIPHER")).

include_na

Include NA values for onset.

verbose

Print messages.

Value

Mapped data.

Named list of HPO IDs.

Named list of HPO IDs.

Functions

  • list_deaths(): map_ List age of death HPO terms

    List age of death phenotypes in the HPO.

  • list_onsets(): map_ List age of onset HPO terms

    List age of onset phenotypes in the HPO.

Examples

deaths <- list_deaths()
#> Translating ontology terms to ids.
onsets <- list_onsets()
#> Translating ontology terms to ids.