[BioC] IPI to entrez id

[Marc Carlson]

Hi Viritha,

The merge function is in base R.

What is the output from your sessionInfo()


  Marc


On 03/09/2011 01:19 PM, viritha kaza wrote:
> Hi Marc,
> Thanks for the explanation.I now realised that there can not be 1:1
> relation between the IPI and the Entrez ids. Like how Dick was saying
> I used both the methods first by the site:
> ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.xrefs.gz.
> and then the remaining with the code in biomart:
> as I had mentioned previously
>  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="")
> # ipi_test file contained the IPI's that I wanted to convert
> >getBM(attributes =
> c("ipi","entrezgene","hgnc_symbol"),filters="ipi",values=ipi,mart =
> ensembl)
> >write.table(ipi_entrez,"ipi_entrez_test.txt",sep='\t')
>  
> I could not find the merge method of yours which dick was mentioning.
> For now I am only interested in the entrez id and genesymbol only for
> the respective IPI in my list.
> Is there an easy method for this and if they could share it, then it
> would be excellent.
> Thanks,
> Viritha