[BioC] ChIPpeakAnno, getAnnotation question

[Zhu, Lihua (Julie)]

Dear Daria,

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_2.0.3.tar.gz at
http://www.bioconductor.org/packages/2.9/bioc/html/ChIPpeakAnno.html (It
will take a couple of days for the version 2.0.3 to appear yet).

Best regards,

Julie

On 8/29/11 1:29 PM, "Daria Goranskaya" <daria.goranskaya at gmail.com> wrote:

> Dear Julie:
> 
> Thank you! Where can I download new version? On bionconductor site
> there is still the old one.
> 
> Best regards,
> Daria
> 
> On Mon, Aug 29, 2011 at 6:46 PM, Zhu, Lihua (Julie)
> <Julie.Zhu at umassmed.edu> wrote:
>> Daria,
>> 
>> The warnings you experienced with 5utr has been fixed and transcript has
>> been added as an option for featureType. Please download the 2.0.2 version.
>> 
>> Thanks for your input!
>> 
>> Best regards,
>> 
>> Julie
>> 
>> 
>> On 8/29/11 10:56 AM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:
>> 
>>> Dear Daria,
>>> 
>>> By default, getAnnotation assumes featureType TSS. Currently, the parameter
>>> featureType accepts one of the feature types (case sensitive):
>>> "TSS","miRNA", "Exon", "5utr", "3utr" or "ExonPlusUtr". For example, 5utr
>>> for 5 UTR.
>>> 
>>> You were right that with parameter featureType set to TSS, getAnnotation
>>> returns the gene coordinates. If you think it is useful to have transcript
>>> coordinates, I will be happy to add featureType transcript. Thanks!
>>> 
>>> Best regards,
>>> 
>>> Julie
>>> 
>>> 
>>> 
>>> 
>>> 
> 
> ********************************
> Dariya Goranskaya
> PhD student
> Unit of Computational Medicine,
> Department of Medicine,
> Karolinska Institutet
> Stockholm, Sweden
> email: dariya.goranskaya at ki.se
>          daria.goranskaya at gmail.com
> Office Number: +46 8 517 708 69
> ********************************