[BioC] chippeakanno:::addGeneID for adding gene symbol etc. to annotatedPeak or enrichedGO

[Zhu, Lihua (Julie)]

Deepak,

Jianhong has added a function addGeneIDs for adding gene symbol,
entrezID...to annotatedPeak or enrichedGO (>=1.9.8). Please let us know how
it works out for you. Many thanks for your invaluable feedback!

For those of you who attended the ChIPpeakAnno workshop in Bioc2011 meeting
last Friday, here is the update per your request (>=1.9.8).

1. Updated documentation for the new function peaksNearBDP (peaks near
bi-directional promoter)
2. Updated documentation for annotatePeakInBatch (defaults are specified)
3. makeVennDiagram function now has a new field called useFeature
(TRUE/FALSE). TRUE means that the overlapping will be calculated using the
feature field in annotatedPeak for deriving overlapping statistics and
drawing diagram. FALSE means that the overlapping will be calculated using
the chromosome ranges as in the previous versions. The default is FALSE for
backward compatibility.

Thanks so much for all your invaluable input and positive feedback!

Best regards,

Julie 


On 7/29/11 10:36 AM, "Deepak Grover.CTR" <Deepak.Grover.CTR at usuhs.mil>
wrote:

> Thank you for the response, Dr. Zhu.
> I will look forward to those updates which bring HUGO sumbols to the table.
> 
> I haven't been able to use the getBM command successfully for mouse gene
> symbols. 
> Can you suggest me what should the syntax be, if you people have already done
> it.
> 
> Thanks again,
> Deepak
> 
> 
> 
> 
> 
> Classification:  UNCLASSIFIED
> Caveats: None
>>>> "Zhu, Lihua (Julie)" <Julie.Zhu at umassmed.edu> 7/28/2011 4:46 PM >>>
> Deepak,
> 
> Jianhong is working on adding gene symbol and other IDs to the annotated
> peaks. We will keep you updated.
> 
> Meanwhile, you could use getBM function in biomaRt to get gene symbols.
> Thanks!
> 
> Best regards,
> 
> Julie 
> 
> 
> On 7/28/11 9:50 AM, "Deepak Grover.CTR" <Deepak.Grover.CTR at usuhs.mil> wrote:
> 
>> Dear Ms. Zhu,
>> 
>> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am trying
>> to
>> employ your bioconductor package for the annotation. I am getting gene IDs in
>> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the same
>> to
>> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix for
>> this.
>> I was trying convert bed format data for mouse gene annotation using
>> "BED2RangedData" but so far did not succeed as that is giving me duplicate
>> row
>> name error.
>> 
>> I will really appreciate if you can suggest an easy fix to my problem.
>> 
>> Best,
>> 
>> 
>> 
>> Deepak Grover, Ph.D.
>> Scientist
>> Department of Anatomy, Physiology & Genetics
>> Uniformed Services University of the Health Sciences
>> Room C-2070
>> 4301 Jones Bridge Rd Bethesda, MD 20814
>> 301-295-3817
>> Deepak.Grover.CTR at usuhs.mil
>> http://www.usuhs.mil/
>>  
>> 
>> 
>> 
>> Classification:  UNCLASSIFIED
>> Caveats: None
>> 
>> 
>> 
>> Classification:  UNCLASSIFIED
>> 
>> Caveats: None
>> 
>> 
>> 
> 
> 
> 
> 
> Classification:  UNCLASSIFIED
> 
> Caveats: None
> 
> 
>