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

[Zhu, Lihua (Julie)]

Dear Jennifer,

I am wondering what is the rational to have multiple coordinates for the
same feature name. We could append a serial number to the feature names with
multiple coordinates in the future release.

Best regards,

Julie


On 1/20/11 8:35 PM, "Chu-Ya (Jennifer) Yang" <chu-ya.yang at lifesci.ucsb.edu>
wrote:

> Dear Prof. Zhu,
> 
> Thank you for the assistance.
> 
> We tried to convert the features with unique names and then convert to
> ranged data format and then convert back to the original names of the
> features.  And then annotate the data with ChIPpeakAnno.  It finally
> worked, and was not easy for us to do.
> 
> Since ChIPpeakAnno is a very powerful annotation algorithm and it is
> very helpful to our data analysis, I am wondering whether it is possible
> that you would please consider to modify the BED2RangedData to
> accommodate more flexibility of the bed files, such as allow multiple
> rows with identical name identifier.
> 
> Thank you,
> 
> Jennifer
> 
> Zhu, Lihua (Julie) said the following on 1/19/2011 2:19 PM:
>> Jennifer,
>> 
>> The name column name=mm9[ ,4] has duplicates (needs to be unique).
>> 
>> Best regards,
>> 
>> Julie
>