[BioC] RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion

[Zhu, Lihua (Julie)]

Mboyba,

The category enhancers/silencers should be potential enhancers/silencers or
just intergenic region. We labeled it as enhancers/silencers initially
because one of our collaborators requested this specifically which lead to
the addition of this function to the ChIPpeakAnno package.

Since you are interested in assignment to intergenic regions as a whole (not
distinguishing different elements within these regions), you can use the
function as it is now, being aware that the category enhancers/silencers is
intergenic region.

Thanks again for the feedback!

Best regards,

Julie


On 4/26/13 11:02 AM, "DIOP M boyba" <Mboyba.DIOP at igr.fr> wrote:

> Hi,
> 
> Thank you for your help.
> Unfortunately I have not enough skills in genomic to help you
> to describe more accurately the intergenic elements.
> 
> Best regards,
> Mboyba
> ________________________________________
> De : Zhu, Lihua (Julie) [Julie.Zhu at umassmed.edu]
> Date d'envoi : jeudi 25 avril 2013 15:27
> À : DIOP M boyba
> Cc: bioconductor at r-project.org
> Objet : Re: ChIPpeakAnno_2.8.0 assignCromosomeRegion
> 
> Dear Mboyba,
> 
> According to my understanding, intergenic regions consist of promoters,
> enhancers/silencers, noncoding RNAs and other unknown elements. Currently,
> any intergenic regions that are not promoter or immediate downstream are
> lumped into enhancer/silencer category. If you could help us define
> enhancers and other intergenic elements more accurately, then we can have a
> fine-grained partition of the intergenic region.
> 
> Many thanks for your input!
> 
> Best regards,
> 
> Julie
> 
> 
> On 4/25/13 5:33 AM, "DIOP M boyba" <Mboyba.DIOP at igr.fr> wrote:
> 
>> Dear Julie,
>> 
>> I am using the version 2.8.0 of your package ChIPpeakAnno.
>> I want to annotate a list of peaks which are in BED format and then to
>> represent their distribution over the genome. To do this I use the
>> assignChromosomeRegion function to annotate my regions. In the results there
>> is 6 features : exon, intron, enhancer/silencer, promoter, 5 prime UTR and 3
>> prime UTR.
>> 
>> My question is where is the intergenic class ?
>> 
>> It is possible to have intergenic regions that are not in promoter or
>> enhancer/silencer so how do you treat this case ?
>> 
>> Best regards,
>> Mboyba
>> 
>> 
>> 
>