Dear Julie,

is the addGeneIDs function available in the current library or just in the
developer version?

thanks
Andreia

On Fri, Aug 5, 2011 at 3:54 AM, Zhu, Lihua (Julie)
<Julie.Zhu@umassmed.edu>wrote:

> 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@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@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@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@usuhs.mil
> >> http://www.usuhs.mil/
> >>
> >>
> >>
> >>
> >> Classification:  UNCLASSIFIED
> >> Caveats: None
> >>
> >>
> >>
> >> Classification:  UNCLASSIFIED
> >>
> >> Caveats: None
> >>
> >>
> >>
> >
> >
> >
> >
> > Classification:  UNCLASSIFIED
> >
> > Caveats: None
> >
> >
> >
>
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>



-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

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