R/mouseSymbol_to_humanEnsembl.r

In neurogenomics/scFlowExamples: Provide example datsets to run scFlow

#########################################################################
#' Convert gene symbols from mouse to human and then to human ensembl IDs
#'
#' @param x Object of class dgCMatrix
#' @param ... additional parameters
#'
#' @import One2One
#' @importFrom biomaRt useMart
#' @importFrom biomaRt getBM
#'
#' @export
mouseSymbol_to_humanEnsembl <- function(x,
                            ...) {

  # Convert gene symbols from mouse to human
  # Limit genes to Mouse:Human orthologs

  mouse2human <- One2One::ortholog_data_Mouse_Human$orthologs_one2one
  rownames(mouse2human) <- mouse2human$mouse.symbol

  x <- x[rownames(x) %in% mouse2human$mouse.symbol,]
  mouse2human2 <- mouse2human[rownames(x),]
  rownames(x) <- mouse2human2$human.symbol

  # Convert human gene symbols to Ensembl gene IDs

  ensembl <- biomaRt::useMart("ensembl",dataset="hsapiens_gene_ensembl")

  hgnc2ensg <- biomaRt::getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id'),
        filters = 'hgnc_symbol',
        values = rownames(x),
        mart = ensembl)

  hgnc2ensg <- as.data.frame(hgnc2ensg, row.names = hgnc2ensg$hgnc_symbol)

  x <- x[rownames(x) %in% hgnc2ensg$hgnc_symbol,]
  hgnc2ensg2 <- hgnc2ensg[rownames(x),]
  rownames(x) <- hgnc2ensg2$ensembl_gene_id

  return(x)

}