[BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion

[Zhu, Lihua (Julie)]

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
> 
> 
>