[BioC] IPI to entrez id

[Dick Beyer]

Hi Viritha,

Marc's one liner seems very simple to do. What errors are you getting when you try this? You could try this

source('http://bioconductor.org/biocLite.R')
biocLite("org.Hs.eg.db")
library(org.Hs.eg.db)
allAnnots <- merge(toTable(org.Hs.egPROSITE), toTable(org.Hs.egGO), by.x="gene_id", by.y="gene_id")

Works for me with R 2.12.2.

I haven't used the ipi.HUMAN.xrefs, I just use this one:

ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/ipi.HUMAN.dat.gz

Hope that helps,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Wed, 9 Mar 2011, 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
> 
>