get_gene_lists: Get gene list

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

Get gene list

Description

This function returns a vector of genes associated with a particular phenotype. It uses the phenotype_to_genes.txt file from the HPO.

Usage

get_gene_lists(
  phenotypes,
  phenotype_to_genes = load_phenotype_to_genes(),
  hpo = get_hpo(),
  as_list = FALSE,
  hpo_id_labels = TRUE
)

Arguments

phenotypes	One or more phenotype name from the HPO (e.g. "Phenotypic abnormality") \<string\>.
phenotype_to_genes	Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
as_list	Return as a named list instead of a data.table.
hpo_id_labels	Label the gene lists with HPO IDs (instead of phenotype names).

Value

a character vector of genes associated with the selected phenotype.

Examples

phenotypes <- c("Focal motor seizure","HP:0000002","HP:0000003")
gene_lists <- get_gene_lists(phenotypes = phenotypes)

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.