[BioC] Gene Name annotation

[Zhu, Lihua (Julie)]

Dear Pablo,

If you type ?annotatePeakInBatch in a R session after library(ChIPpeakAnno),
you will notice that you can annotate your peaks with your own annotation or
built-in annotation dataset.

The following are a few built-in annotation datasets.
 data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37), data(GO.rat.RGSC3.4) and
data(TSS.zebrafish.Zv8). You probably already notice that the main ID of the
built-in dataset is Ensembl_ID. You could use getBM function in biomaRt
package to convert ensembl_ID to gene name or other IDs if needed.

Best regards,

Julie 


On 1/19/11 2:10 PM, "Pablo Echeverria" <Pablo.Echeverria at unige.ch> wrote:

> Dear Julie,
> 
> I'm starting using ChIPpeakAnno.
> I'm analyzing chip-seq data, comparing datasets from my lab and other
> and I mainly would like to obtain from the bed files that I'm using,
> some of the features that are described in your paper (those are already
> working), but also I need to retrieve gene names associated to my peaks.
> 
> How can I get, and excel file with the associated gene name to the
> enriched peaks.
> Could you give the lines that I have to write to get those tables?
> 
> Thank you in advance,
> 
> Pablo
>