Load phenotype_to_genes — load_phenotype_to

This is a function for loading the HPO phenotype to genes text file from HPO. It adds the column names and returns as a dataframe. It contains phenotypes annotated with associated genes.

load_phenotype_to_genes(
  file = c("phenotype_to_genes.txt", "genes_to_phenotype.txt", "phenotype.hpoa"),
  save_dir = file.path(KGExplorer::cache_dir(package = "HPOExplorer"), "data"),
  repo = paste("obophenotype", "human-phenotype-ontology", sep = "/"),
  tag = "latest",
  overwrite = FALSE,
  save_tmp = TRUE,
  verbose = TRUE
)

Source

HPO source data

Arguments

file: name or vector of names of files to be downloaded. If NULL, all assets attached to the release will be downloaded.
save_dir: Folder where the phenotype to genes text file is/will be stored.
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.
save_tmp: Keep the intermediate annotation text file (before it gets converted to .rds format).
verbose: Print messages.

Value

A data.table of the HPO annotations.

Examples

phenotype_to_genes <- load_phenotype_to_genes()
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12