These R code snippets are used to convert between Entrez and Ensembl IDs using biomart web-service. it just exploits the functionalities offered by the biomaRt package. The code is implemented to call the Biomart web-service each time. you can make it more general by calling the first four lines separatly and just passing the "hsp" variable to f…

gistfile1.r

#Usage example:
#EntrezID<-c("2114","9757","5886","9373","6921","4088","7006","6196","10054","10945")
#EnsemblID<-EntrezToEnsembl(EntrezID)

EntrezToEnsembl<-function(EntrezID){
  require(biomaRt);
  ensemble<-useMart("ensembl");
  hsp<-useDataset(mart=ensemble,dataset="hsapiens_gene_ensembl");
  ids<-getBM(filters= "entrezgene",
              attributes= c("entrezgene","ensembl_gene_id", "external_gene_id","description"),
              values= EntrezID, mart= hsp);
  return(ids);
}

gistfile2.r

#Usage example:
#EnsemblID<-c("ENSG00000164548","ENSG00000118515","ENSG00000105705","ENSG00000177414","ENSG00000108179")
#EntrezID<-EnsemblToEntrez(EnsemblID)

EnsemblToEntrez<-function(EnsemblIDs){
        require(biomaRt)
	ensemble<-useMart("ensembl")
	hsp<-useDataset(mart=ensemble,dataset="hsapiens_gene_ensembl")
	ids<-getBM(filters= "ensembl_gene_id",
                   attributes= c("ensembl_gene_id", "external_gene_id", "entrezgene", "description"),
                   values= EnsemblIDs, mart= hsp)
	return(ids)
}

gistfile3.r

EntrezToHGNC<-function(EntrezID){
  require(biomaRt);
  ensemble<-useMart("ensembl");
  hsp<-useDataset(mart=ensemble,dataset="hsapiens_gene_ensembl");
  ids<-getBM(filters= "entrezgene",
              attributes= c("entrezgene","hgnc_id", "hgnc_symbol","description"),
              values= EntrezID, mart= hsp);
  return(ids);
}