[BioC] Biomart annotation

jarod_v6 at libero.it jarod_v6 at libero.it
Fri Jul 18 11:27:47 CEST 2014


Hi there!
I need to convert all my ensemble gene id on  hgnc symbols and entrez gene id. 
My ensemble release s the n°72.


I use this script:

dif.DEs$ensembl <- sapply(strsplit(rownames(dif.DEs),split="nn+"),"[",1)
#use biomart
library( "biomaRt" )
ensembl = useMart( host="jun2013.archive.ensembl.org",biomart="
ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl" )
genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene", 
"hgnc_symbol"),
                  filters = "ensembl_gene_id",
                  values = dif.DEs$ensembl,
                  mart = ensembl )
idx <- match(dif.DEs$ensembl, genemap$ensembl_gene_id )
dif.DEs$entrez <- genemap$entrezgene[ idx ]
dif.DEs$hgnc_symbol <- genemap$hgnc_symbol[ idx ]


dif.DEs$entrez
 [1]  25870  89869  54465   2840     NA  80230  57673 123264     NA     NA
[11]     NA 392364     NA     NA     NA     NA 221883     NA     NA     NA
[21]     NA     NA     NA     NA

Many of that are as NA. How can I annotate all the genes?
thanks in advance for  any help!



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