gpt_annot_read: Read annotations from GPT

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

Read annotations from GPT

Description

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

Usage

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()

neurogenomics/HPOExplorer documentation built on July 17, 2024, 3:12 p.m.