[BioC] mypeaklist in ChIPpeakAnno

[Zhu, Julie]

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:
>> Dear Ramu,
>> 
>> You can use read.table to read the data in bed file format from MACS, then
>> use BED2RangedData to convert the data to RangedData.
>> 
>> Library(ChIPpeakAnno)
>> X = read.table("mypeak.bed",sep="\t")
>> MyPeakList = BED2RangeData(X)
>> 
>> ?BED2RangedData
>> 
>> BTW, I am on vacation so may not be able to check email frequently.
>> 
>> Kind regards,
>> 
>> Julie
>> 
>> 
>> On 8/13/10 3:44 AM, "Ramu Chenna" <ramu.chenna at biotec.tu-dresden.de> wrote:
>> 
>>   
>>> Dear Julie,
>>> 
>>> The link did not work, but I found the ppt.  Thanks.
>>> 
>>> I am not a R geek, and I just need to know how to read MACS output
>>> as say 'myPeakList' as RangedData. It would be nice to know there is already
>>> a R function doing this.
>>> 
>>> Regards,
>>> Ramu
>>> 
>>> Zhu, Julie wrote:
>>>     
>>>> Dear Ramu,
>>>> 
>>>> It is a RangedData. Please take a look at the 2nd example given in the
>>>> Bioc2010 meeting in Seattle.
>>>> 
http://www.bioconductor.org/help/course-materials/2010/BioC2010/BioC2010_Ch>>>>
I
>>>> PpeakAnno.pdf
>>>> 
>>>> 
>>>>   
>>>> 
>>>>   
>>>>       
>> 
>> 
>>   
>