R/get_hgnc.R

In isglobal-brge/EDY: Analysis of extreme downregulation of chromosome Y (EDY)

#' Obtaining HUGO gene nomenclature committee (hgnc) symbol from genBank
#' accession numbers, entrezgenes (NCBI gene IDs), RefSeq IDs, UniProt IDs or
#' Ensembl stable IDs.
#'
#' @title Get hgnc symbol
#' @param x An ExpressionSet, a RangedSummarizedExperiment or a vector of IDs.
#' @param key.type A string indicating the type of gene ID that we want to get
#'   hgnc symbol from. It must be one of \code{refseq, uniprot, ensembl,
#'   entrezgene} or \code{genbank}.
#' @param key.col A string indicating the name of the column that contains the
#'   \code{key.type} in the table of features of the ExpressionSet (accessed by
#'   \code{fData}) or in the metadata of the rows in the
#'   RangedSummarizedExperiment (accessed by \code{rowData}).
#' 
#' @import org.Hs.eg.db
#' @export get_hgnc 
#' @return In case \code{x} is a vector, the output is another vector with the
#'   hgnc symbols and the query IDs as names. Otherwise, the output is an
#'   \code{ExpressionSet} or \code{RangedSummarizedExperiment} containing the
#'   previous information in \code{x} plus the column \code{hgnc_symbol}
#'   containing the gene symbols.

get_hgnc <- function(x, key.type, key.col, ...){
  
  object.type <- class(x)[1]
  if (object.type == "ExpressionSet"){
    fData(x)$id.feature <- featureNames(x)
    query <- fData(x)[, key.col]
  } else if (object.type == "RangedSummarizedExperiment"){
    colData(x)$id.feature <- rownames(assay(x))
    query <- colData(x)[, key.col]
  } else {
    query <- x
  } 
  
  key.type <- tolower(key.type)
  key.types <- c("refseq", "uniprot", "ensembl", "entrezgene" )
  
  if (!(key.type%in%key.types) && key.type!="genbank"){
    stop("Invalid key.type. Allowed choices are: 'refseq', 'uniprot', 'ensembl', 'entrezgene' 
         and 'genbank'")
  }
  #Get entrezgene from id
  else if (key.type%in%key.types){
    dictionary <- EDY::genome.annot$hgnc_symbol
    names(dictionary) <- EDY::genome.annot[, key.type]
    hgnc_symbol <- unname(dictionary[query])
    #Join to fData
    if (object.type == "ExpressionSet"){
      fData(x) <- cbind(hgnc_symbol, fData(x))
    } else if (object.type == "RangedSummarizedExperiment"){
      rowData(x) <- cbind(hgnc_symbol, rowData(x))
    } else {
      x <- dictionary[query]
      }
    }
  else if (key.type=="genbank"){ 
      list_entrez_id <- as.list(org.Hs.egACCNUM2EG) 
      
      GB.ids <- names(list_entrez_id)  
      dictionary <- unlist(list_entrez_id)
      names(dictionary) <- GB.ids
    
      entrezgenes <- unname(dictionary[query])
      
      dictionary2 <- EDY::genome.annot$hgnc_symbol
      names(dictionary2) <- EDY::genome.annot$entrezgene
      hgnc_symbol <- unname(dictionary2[entrezgenes])
     
      #Join to fData
      if (object.type == "ExpressionSet"){
        fData(x) <- cbind(hgnc_symbol, fData(x))
        } else if (object.type == "RangedSummarizedExperiment"){
        rowData(x) <- cbind(hgnc_symbol, rowData(x))
        } else {
          x <- dictionary2[entrezgenes]
        }
  }
  
  #output
  x
}