[BioC] chippeakanno related

[Zhu, Lihua (Julie)]

Deepak,

Your file is not in bed file format. Please check out the bed file format
definition at
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

Here is an related post
http://comments.gmane.org/gmane.science.biology.informatics.conductor/28493

I will keep you posted on the new function. Thanks!

Best regards,

Julie


On 8/2/11 12:47 PM, "Deepak Grover.CTR" <Deepak.Grover.CTR at usuhs.mil> wrote:

> Dear Dr. Zhu,
> 
> Thank you, the conversion will be incredible to have and I will await your
> response.
> 
> Meanwhile, I am finding an error while doing the following. Can you suggest a
> fix for this.
> I really appreciate your response as it will help me to annotate my chip-seq
> data.
> 
> x <- 
> read.table(file="~/projects/chip-seq/H3K4/C2C12-Control-H3K4-W200-G2000-FDR0.0
> 1-island.bed")
> 
> x <- BED2RangedData(x)
> Error in `rownames<-`(`*tmp*`, value = c("155", "113", "240", "486", "128",  :
>   duplicate rownames not allowed
> 
> attached is the file, if needed.
> 
> 
> Thanks,
> Deepak
> 
> 
>>>> "Zhu, Lihua (Julie)"  8/1/2011 10:22 AM >>>
> Deepak,
> 
> Sorry for the late response! I just got back from the Bioc2011 conference.
> 
> We hope to add the conversion function this week. So I think it is the best
> to wait and I will keep you updated!
> 
> Best regards,
> 
> Julie
> 
> 
> On 7/29/11 10:36 AM, "Deepak Grover.CTR"
> wrote:
> 
>> Thank you for the response, Dr. Zhu.
>> I will look forward to those updates which bring HUGO sumbols to the table.
>> 
>> I haven't been able to use the getBM command successfully for mouse gene
>> symbols. 
>> Can you suggest me what should the syntax be, if you people have already done
>> it.
>> 
>> Thanks again,
>> Deepak
>> 
>> 
>> 
>> 
>> 
>> Classification:  UNCLASSIFIED
>> Caveats: None
>>>>> "Zhu, Lihua (Julie)"  7/28/2011 4:46 PM >>>
>> Deepak,
>> 
>> Jianhong is working on adding gene symbol and other IDs to the annotated
>> peaks. We will keep you updated.
>> 
>> Meanwhile, you could use getBM function in biomaRt to get gene symbols.
>> Thanks!
>> 
>> Best regards,
>> 
>> Julie 
>> 
>> 
>> On 7/28/11 9:50 AM, "Deepak Grover.CTR"  wrote:
>> 
>>> Dear Ms. Zhu,
>>> 
>>> I am a researcher working on mouse chip-seq at USUHS, bethesda. I am trying
>>> to
>>> employ your bioconductor package for the annotation. I am getting gene IDs
>>> in
>>> ensembl format using TSS.mouse.NCBIM37, however I am looking to do the same
>>> to
>>> get back gene symbols(HUGP/hgnc). Can you suggest if there is a quickfix for
>>> this.
>>> I was trying convert bed format data for mouse gene annotation using
>>> "BED2RangedData" but so far did not succeed as that is giving me duplicate
>>> row
>>> name error.
>>> 
>>> I will really appreciate if you can suggest an easy fix to my problem.
>>> 
>>> Best,
>>> 
>>> 
>>> 
>>> Deepak Grover, Ph.D.
>>> Scientist
>>> Department of Anatomy, Physiology & Genetics
>>> Uniformed Services University of the Health Sciences
>>> Room C-2070
>>> 4301 Jones Bridge Rd Bethesda, MD 20814
>>> 301-295-3817
>>> Deepak.Grover.CTR at usuhs.mil
>>> http://www.usuhs.mil/
>>>  
>>> 
>>> 
>>> 
>>> Classification:  UNCLASSIFIED
>>> Caveats: None
>>> 
>>> 
>>> 
>>> Classification:  UNCLASSIFIED
>>> 
>>> Caveats: None
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> 
>> Classification:  UNCLASSIFIED
>> 
>> Caveats: None
>> 
>> 
>> 
> 
> 
> 
>  
>   
>  
> Classification:  UNCLASSIFIED Caveats: None   ­­