[BioC] Annotating HGU133plus2 genes with number of coding changes

[Steffen Durinck]

Hi Marco,

You can do this with the biomaRt package (use the devel version, >= 
1.9.21) , here's how:

library(biomaRt)
mart=useMart("ensembl", dataset="hsapiens_gene_ensembl")
getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","synonymous_snp_count","non_synonymous_snp_count"), 
filters="affy_hg_u133_plus_2", values=c("201746_at","231640_at"), mart=mart)

it will give:

ensembl_gene_id ensembl_transcript_id synonymous_snp_count 
non_synonymous_snp_count
1 ENSG00000141510       ENST00000269305                    
5                       20
2 ENSG00000133703       ENST00000256078                    
1                        1
3 ENSG00000133703       ENST00000311936                    
1                        1


Unfortunately you won't be able to get the affy id in the output but you 
can use biomaRt to map the Ensembl ids in the output back to the afffy ids.

Cheers,
Steffen


marco zucchelli wrote:
> Hi,
>
>  I was wondering if it exists an annotation package for Affy 133plus2
> reporting the number of synonymous & non synonymous changes for the
> genes on the array.
>
> If it does not exist does anybody has a good suggestion  about how to
> retrive this information from databases ?
>
>
> Marco
>
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