[BioC] Gene Name annotation with ChIPpeakAnno

[Zhu, Lihua (Julie)]

Dear Pablo,

It is great that you got the annotated peaks now. To add additional
annotation such as gene symbol to the annotatedPeak, I would suggest do the
following,

Ann.peaks = as.data.frame(annotatedPeak)

Then merge Ann.peaks with the annotation data containing gene symbol and
ensembl ID etc obtained from getBM function in biomaRt package. If you
encounter problem using getBM, please email the bioconductor list and
biomaRt developer with the code, error message and session information.

Best regards,

Julie


On 1/20/11 7:32 AM, "Pablo Echeverria" <Pablo.Echeverria at unige.ch> wrote:

> Dear Julie,
> thanks for your help.
> I've been trying, but not good results.
> 
> let's say I have my bed file in my desktop. Then I type the following:
> 
>> library(ChIPpeakAnno)
>> erchip.bed=read.table("~/Desktop/erchip.bed", sep="\t", skip=1,
> header=FALSE)
>> myPeakList = BED2RangedData(erchip.bed,header=FALSE)
>> data(TSS.human.NCBI36)
>> annotatedPeak = annotatePeakInBatch (myPeakList, AnnotationData =
> TSS.human.NCBI36)
> 
> so far is OK. I've been trying to use the function getBM to get in
> addition to Ensembl IDs the gene symbols, as well. But nothing worked.
> If I want to write a table with these peaks associated with gene
> symbols (human)...what should I type after those previous lines?
> 
> Thank you again,
> Best regards,
> 
> Pablo
> On 19 janv. 11, at 20:58, Zhu, Lihua (Julie) wrote:
> 
>> 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
> 
>