[BioC] ensembl to NCBI Mapping

[James W. MacDonald]

Hi Neeba,

On 6/21/2013 3:21 AM, Neeba Dijo wrote:
> H
> i Team
>
> I have set of genes protein and transcripts from ensembl for homo sapiens
> and
>
> I have to map these ensembl  gene , protein and
> transcript ID to the coressponding gene ID from NCBI

If I assume that you mean Gene ID (what used to be called the Entrez 
Gene ID), then this is a simple thing to do. You will need the 
org.Hs.eg.db package, and will need to use the select function. As an 
example, let's say I have a vector of Ensembl transcript IDs, like so:

 > trans
[1] "ENST00000596924" "ENST00000263100" "ENST00000595014" "ENST00000598345"
[5] "ENST00000600966" "ENST00000543436"

And you want to know the Gene ID. You just do:

 > library(org.Hs.eg.db)
 > select(org.Hs.eg.db, trans, "ENTREZID", "ENSEMBLTRANS")
      ENSEMBLTRANS ENTREZID
1 ENST00000596924        1
2 ENST00000263100        1
3 ENST00000595014        1
4 ENST00000598345        1
5 ENST00000600966        1
6 ENST00000543436        2

As it appears you are new to R, I would highly recommend reading An 
Introduction To R 
(http://cran.r-project.org/doc/manuals/r-release/R-intro.html) and the 
vignette for AnnotationDbi 
(http://bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf).

Best,

Jim



>
>
> I heard that bio conductor do this. Can you explain where I got this . how
> can i do that
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099