R/get.SYMBOL.R

In AEBilgrau/Bmisc: Biostatistical miscellaneous functions

#' Get Hugo gene symbols and ensembl gene identifiers
#' 
#' These functions uses biomaRt to get gene symbols and ensembl gene identifies 
#' for an ExpressionSet object.
#' 
#' @param es in an ExpressionSet object
#' @param subset is a character vector of feature names.
#' @param attributes other attributes to extract. A possible list of attributes
#'   can be retrieved using the function \code{listAttributes}.
#' @param \dots arguments passed to \code{getBM}.
#' @return  a \code{data.frame} with columns corresponding to the matched gene identifiers.
#' @author Anders Ellern Bilgrau <anders.ellern.bilgrau (at) gmail.com>
#' @importFrom Biobase featureNames
#' @importFrom biomaRt useMart useDataset getBM
#' @export
get.SYMBOL <- function(es,
                       subset = featureNames(es), 
                       attributes = NULL, 
                       ...) {
  if (!requireNamespace("biomaRt")) {
    stop("The package biomaRt is required to use the function.")
  }
  mart <- useMart("ensembl")
  ensembl <- useDataset("hasapiens_gene_ensembl", mart = mart)
  res <- 
    getBM(attributes = c(get.attribute(es), "hgnc_symbol", 
                         "ensembl_gene_id", attributes),
          filters = get.attribute(es),
          values = subset,
          mart = ensembl, ...)
  colnames(res) <- c("Probe", "GENE", "ENSG")
  return(res)
}