[BioC] ChIPpeakAnno_2.8.0 assignCromosomeRegion
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Thu Apr 25 15:27:30 CEST 2013
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
>
>
>
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