Hi,

I wanted a table that provides a mapping from Entrez Ids to Gene Symbols for homo sapiens. To do this, I used the following code:

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library(org.Hs.eg.db)

   x <- org.Hs.egSYMBOL
   # Get the gene symbol that are mapped to an entrez gene identifiers
   mapped_genes <- mappedkeys(x)
   # Convert to a list
   xx <- as.list(x[mapped_genes])
   eids <- ''

   ENTREZID2GENESYMBOL <- matrix(0,length(xx),2)
   colnames(ENTREZID2GENESYMBOL) <- c('ENTREZ_IDS','GENE_SYMBOLS')
   for(k in 1:length(xx)){
        if(k==1){
          eids <- unlist(xx[k])
          goids <- names(xx[k])
        }
        if(k>1){
          eids <- c(eids,unlist(xx[k]))
          goids <- c(goids,names(xx[k]))
        }
        dd <- ''
        for(m in 1:length(unlist(xx[k]))){
          if(m==1)
            dd <- unlist(xx[k])[m]
          if(m>1)
            dd <- paste(dd,unlist(xx[k])[m],sep=',')
        }
        ENTREZID2GENESYMBOL[k,2] <- dd
    }
    ENTREZID2GENESYMBOL[,1] <- rownames(ENTREZID2GENESYMBOL) <- goids
    idx <- unlist(sort(as.numeric(rownames(ENTREZID2GENESYMBOL)),index=TRUE)[2])
    ENTREZID2GENESYMBOL <- ENTREZID2GENESYMBOL[idx,]
    
    write.table(ENTREZID2GENESYMBOL,'test.txt',sep='\t')

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However, when I search the table for the gene 'mTOR' I don't find anything. I believe that mTOR is widely recognized as a cancer causing gene, and I was wondering if I was doing something wrong in my code (or libraries/functions used)...

many thanks!

Tim


PS: My sessionInfo() is :

R version 2.8.0 (2008-10-20) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] org.Hs.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.4.2 Biobase_2.2.1      
> 


      
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