R/get_gene_list.R

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

#' Get gene list
#'
#' This function returns a vector of genes associated with a particular phenotype.
#' It uses the \code{phenotype_to_genes.txt} file from the hpo.
#'
#' @param phenotype A phenotype (name) from the HPO
#' (e.g. "Phenotypic abnormality") <string>
#' @param phenotype_to_genes The phenotype_to_genes.txt file from HPO that
#' contains gene annotations for HPO phenotypes.
#' @returns a character vector of genes associated with the selected phenotype.
#' @example \dontrun{
#' # Creating a list of gene lists indexed by phenotype name
#' GeneLists <- list()
#' for (p in Phenotypes) {
#'   GeneLists[[p]] <- get_gene_list(p,phenotype_to_genes)
#' }}
#' @export
get_gene_list <- function(phenotype, phenotype_to_genes) {
  return(phenotype_to_genes$Gene[phenotype_to_genes$Phenotype == phenotype])
}