Read annotations from GPT — gpt_annot

Read in phenotype annotations generated by GPT and do some initial preprocessing (e.g. adding HPO IDs).

gpt_annot_read(
  save_dir = KGExplorer::cache_dir(package = "HPOExplorer"),
  phenotype_to_genes = load_phenotype_to_genes(save_dir = save_dir),
  force_new = FALSE,
  hpo = get_hpo(),
  include_nogenes = TRUE,
  verbose = TRUE,
  ...
)

Arguments

save_dir

Directory to save a file to.

phenotype_to_genes

Output of load_phenotype_to_genes mapping phenotypes to gene annotations.

force_new

If TRUE, the data will be downloaded from GitHub even if it already exists locally.

hpo

Human Phenotype Ontology object, loaded from get_ontology.

include_nogenes

Include phenotypes with no associated genes.

verbose

Print messages.

...

Arguments passed on to get_data

add_version: Add the release version to the returned object's attributes
file: name or vector of names of files to be downloaded. If NULL, all assets attached to the release will be downloaded.
repo: Repository name in format "owner/repo". Defaults to guess_repo().
tag: tag for the GitHub release to which this data should be attached.
overwrite: Should any local files of the same name be overwritten? default TRUE.

Value

data.table of phenotype annotations

Examples

gpt_annot <- gpt_annot_read()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-04-26
#> 256 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,879 phenotypes.