Hi Khademul,

Thank you very much for the great suggestions!

I have implemented BED2RangedData as well as GFF2RangedData in
ChIPpeakAnno_1.2.2 for converting BED/GFF format to RangedData before
calling annotatePeakInBatch. Please let me know if you encounter any
problems. Thanks!

Best regards,

Julie
> 
> 
> On 11/27/09 12:12 PM, "Khademul Islam" <khademul.islam@gmail.com> wrote:
> 
>> Hello Dr. Julie,
>> 
>> 
>> It would be really really helpful, specially who has only little knowledge
>> about R, if you impliment "bed2RangedData" function. It will be pretty
>> straight forward use of the bed file that is generated by peak calling
>> softwares.
>> 
>> If you already have version with this function, I would be happy to
>> try..............
>> 
>> Thanks again
>> 
>> Khademul
>> 
> 
> *******************************************
> Lihua Julie Zhu, Ph.D
> Research Associate Professor
> Program Gene Function and Expression
> Program in Molecular Medicine
> University of Massachusetts Medical School
> 364 Plantation Street, Room 613
> Worcester, MA 01605
> 508-856-5256
> http://www.umassmed.edu/pgfe/faculty/zhu.cfm
> 
> 
>> 


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