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

[Zhu, Lihua (Julie)]

Deepak,

You could download the most recent version from the repository using svn.
 svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChIPpeakAnno/

Alternatively, you could download ChIPpeakAnno_1.9.9.tar.gz at
http://www.bioconductor.org/packages/2.9/bioc/html/ChIPpeakAnno.html (It
will take a couple of days for the version 1.9.9 to appear yet).

For documentation please type the following commands in a R session
Library(ChIPpeakAnno)
browseVignettes("ChIPpeakAnno")
Or refer to 
http://www.bioconductor.org/packages/2.9/bioc/vignettes/ChIPpeakAnno/inst/do
c/ChIPpeakAnno.pdf

Best regards,

Julie


On 8/5/11 11:59 AM, "Deepak Grover.CTR" <Deepak.Grover.CTR at usuhs.mil> wrote:

> Thank you for the update Dr. Zhu. I am looking forward to work with this.
> Can you point me to place where I can access the updated version of your
> package and documentation.
> 
> Best,
> Deepak
> 
> 
> 
> 
> 
> Classification:  UNCLASSIFIED
> Caveats: None
>>>> "Zhu, Lihua (Julie)" <Julie.Zhu at umassmed.edu> 8/4/2011 10:54 PM >>>
> 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
>> 
>> 
>> 
> 
> 
> 
> 
> Classification:  UNCLASSIFIED
> 
> Caveats: None
> 
> 
>