[BioC] Need assistance with the file preparation for ChIPpeakAnno. (Jennifer Yang from University of California, Santa Barbara)

[Zhu, Lihua (Julie)]

Jennifer,

Please use Bed2RangedData function. Thanks!

Please also take a look at the following post
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/28497

Best regards,

Julie


On 1/19/11 12:48 PM, "Chu-Ya (Jennifer) Yang" <chu-ya.yang at lifesci.ucsb.edu>
wrote:

> Dear Prof. Zhu,
> 
>  From the example on the 3rd page of "The ChIPpeakAnno user's guide", it
> seems that the user can pass custom annotation data into the function
> annotatePeakInBatch.  I tried to pass a custom annotation data file with
> the following commands,
> 
>> mm9=read.table("/home/Jennifer/mm9_bed/mm9.bed",header=FALSE)
>> Reference=RangedData(IRanges(start=[ ,2], end=[ ,3], names=[ ,4],
> space=[ ,1], strand=[ ,6])
> Error: unexpected '[' in "Reference=RangedData(IRanges(start=["
>> 
> 
> I am wondering how I should define the vector so that the bed format can
> be converted into RangedData with this approach.
> 
> Thank you,
> 
> Jennifer
> 
> Zhu, Lihua (Julie) said the following on 1/18/2011 9:19 AM:
>> Dear Jennifer,
>> 
>> You may also want to contact the data provider as well.
>> 
>> Best regards,
>> 
>> Julie
>