R/convert_genes.R

In Chris-Cherry/sctools: Single cell analysis tools package

#' Convert genes between symbol types
#'
#' Takes an input of genes and converts from inputed type to desired type
#' 
#' @param genes The genes to convert.
#' @param from  Gene symbol type of the input
#' @param to    Desired gene symbol type for the output
#' @param mirror Mirror to use if redirect from primary site required
#' @importFrom biomaRt useMart
#' @importFrom biomaRt getLDS
#'
#' @return Data frame of genes with original and corresponding converted symbols
#' @export


convert_genes <- function(genes, from, to, mirror = "http://useast.ensembl.org/"){
    if (from == 'ENSMUSG'){
        srcMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
        sourceAtts =  'ensembl_gene_id'   
    }
    if (from == 'ENSG'){
        srcMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
        sourceAtts = 'ensembl_gene_id'
    }
    if (from == 'MGI'){
        srcMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
        sourceAtts = 'mgi_symbol'    
    }
    if (from == 'HGNC'){
        srcMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
        sourceAtts = 'hgnc_symbol'
    }
    if (to == 'MGI'){
        tarMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
        tarAtts = 'mgi_symbol'
    }
    if (to == 'HGNC'){
        tarMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
        tarAtts = 'hgnc_symbol'
    }
    genesV2 = biomaRt::getLDS(attributes = sourceAtts, filters = sourceAtts,
                     values = genes, mart = srcMart, 
                     attributesL = tarAtts, martL = tarMart,
                     uniqueRows = F)
    return(genesV2)
}