This function returns a vector of genes associated with a
particular phenotype.
It uses the phenotype_to_genes.txt
file from the HPO.
get_gene_lists(
phenotypes,
phenotype_to_genes = load_phenotype_to_genes(),
hpo = get_hpo(),
as_list = FALSE,
hpo_id_labels = TRUE
)
One or more phenotype name from the HPO (e.g. "Phenotypic abnormality") \<string\>.
Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
Human Phenotype Ontology object, loaded from get_ontology.
Return as a named list instead of a data.table.
Label the gene lists with HPO IDs (instead of phenotype names).
a character vector of genes associated with the selected phenotype.
phenotypes <- c("Focal motor seizure","HP:0000002","HP:0000003")
gene_lists <- get_gene_lists(phenotypes = phenotypes)
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12