[BioC] mypeaklist in ChIPpeakAnno

[Zhu, Julie]

Dear Ramu,

I would suggest download the CpG island track from UCSC and make a
RangedData, then annotate your binding sites with the CpG island.

Kind regards,

Julie


On 8/17/10 4:00 AM, "Ramu Chenna" <ramu.chenna at biotec.tu-dresden.de> wrote:

> Dear Julie,
> 
> Is there way way to classify binding sites into classify promotors
> into cpg-island and non-cpg islands?
> 
> Best
> Ramu
> 
> Zhu, Julie wrote:
>> Dear Ramu,
>> 
>> Glad it worked. Thanks for letting me know!
>> 
>> Kind regards,
>> 
>> Julie
>> 
>> 
>> On 8/16/10 5:44 AM, "Ramu Chenna" <ramu.chenna at biotec.tu-dresden.de> wrote:
>> 
>>   
>>> Dear Julie
>>> 
>>> It works, thanks.  Basically what we wanted to do is, from the peak
>>> list, we want to know
>>> how many peaks are in promotor regions and further classify them into
>>> cpg island promotors and
>>> non-cpg island promoters.
>>> 
>>> Note:  The pdf documentation is not done correct there are lines that are
>>> truncated,  (may be a problem in setting the margin in latex?)
>>> 
>>> Best,
>>> Ramu
>>> 
>>> Zhu, Julie wrote:
>>>     
>>> 
>