R/Uniprot2EG.R

In GuangchuangYu/bitr: Biological Id TranslatoR

##' Convert uniprot ID to entrez gene id
##'
##'
##' @title Uniprot2EG
##' @param uniprot uniprot id
##' @param organism only human supported now
##' @param getDescription get gene description or not
##' @param useBiomart using Biomart to query or using annotation packages.
##' @return a data.frame for mapping
##' @importFrom biomaRt getBM
##' @importFrom biomaRt useMart
##' @export
##' @author Guangchuang Yu \url{http://ygc.name}
Uniprot2EG <- function(uniprot, organism = "human", getDescription=FALSE, useBiomart=TRUE) {
    if (useBiomart == TRUE) {
        ##require(biomaRt)
        if (organism == "human") {
            wh_dataset = "hsapiens_gene_ensembl"
        } else if (organism == "mouse") {
            wh_dataset = "mmusculus_gene_ensembl"
        } else if (organism == "rat") {
            wh_dataset = "rnorvegicus_gene_ensembl"
        } else {
            stop ("Not supported yet...\n")
        }
        ensembl = useMart("ensembl", dataset=wh_dataset)


        if (getDescription) {
            ## UniProt/SwissProt Accession
            eg <- getBM(attributes=c("uniprot_swissprot_accession",
                        "entrezgene", "description"),
                        filters="uniprot_swissprot_accession",
                        values=uniprot, mart=ensembl)

            idx.notMap <- is.na(eg[,2])
            if( any(idx.notMap) ) {
                ## Uniprot/TrEMBL Accession
                ## uniprot_sptrembl
                eg2 <- getBM(attributes=c("uniprot_sptrembl",
                             "entrezgene", "description"),
                             filters="uniprot_sptrembl",
                             values=as.character(eg[idx.notMap, 1]),
                             mart=ensembl)
            }
        } else {
            eg <- getBM(attributes=c("uniprot_swissprot_accession",
                        "entrezgene"),
                        filters="uniprot_swissprot_accession",
                        values=uniprot, mart=ensembl)

            idx.notMap <- is.na(eg[,2])
            if( any(idx.notMap) ) {
                ## Uniprot/TrEMBL Accession
                ## uniprot_sptrembl
                eg2 <- getBM(attributes=c("uniprot_sptrembl",
                             "entrezgene", "description"),
                             filters="uniprot_sptrembl",
                             values=as.character(eg[idx.notMap, 1]),
                             mart=ensembl)

            }
        }

        names(eg)[1] <- "uniprot"
        if( any(idx.notMap) ) {
            names(eg2)[1] <- "uniprot"
            result <- rbind(eg, eg2)
        } else {
            result <- eg
        }
        result <- result[!is.na(result[,2]),]
        result <- result[result[,2] != "",]
        result <- unique(result)

    } else {



    }
    return (result)
}