[BioC] IPI to entrez id

[Samuel GRANJEAUD - IR/ICIM]

Hi,

Could you give us a list of 10 unmatched?

BR

viritha kaza wrote:
> Hi
> thanks for the reply:
> As samuel suggested I used the following link
> ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.xrefs.gz.
> For the once I didnot find,I used the following code
>  
> Though I still dont get 1:1 mapping, I got the entrez and the gene 
> symbol.The ipi_test file contains the list of IPI that I want to convert.
>  
> code:
> >source('http://bioconductor.org/biocLite.R')
> > biocLite("biomaRt")
> >library("biomaRt")
>  >ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") 
> >ipi=scan("ipi_test.txt",what =character(),sep='\n',quote="")
> >getBM(attributes = 
> c("ipi","entrezgene","hgnc_symbol"),filters="ipi",values=ipi,mart = 
> ensembl)
> >write.table(ipi_entrez,"ipi_entrez_test.txt",sep='\t')
>  
> I am still not getting a few.Is there any other method or should I 
> think that those IPI numbers dont have corresponding gene symbols?
> Thanks,
> Viritha

-- 

Samuel GRANJEAUD                   granjeau at tagc.univ-mrs.fr
INSERM - ICIM - TAGC               Tel: +33  (0)491 82 87 11/24
http://tagc.univ-mrs.fr            Fax: +33  (0)491 82 87 01
http://icim.marseille.inserm.fr/proteomique