[BioC] ChIPpeakAnno annotatePeakInBatch

[Zhu, Lihua (Julie)]

Dear Carl,

Yes, you can use ChIPpeakAnno::annotatePeakInBatch to determine the distance
from each DM site to the nearest gene - as measured from the DM site to the
nearest end of the gene by setting the parameter FeatureLocForDistance =
'geneEnd'.

Do you mind sharing your insight about using gene end instead of TSS?
Thanks!

Best regards,

Julie


On 5/17/12 2:43 AM, "Carl Baribault" <cbaribau at tulane.edu> wrote:

> Dear Dr. Zhu,
> 
> First, thank you and your colleagues for all your efforts in
> developing the subject R package.
> 
> I have two bed files containing
> significantly-differentially-methylated- (or DM) sites and genes,
> respectively.
> 
> I'd like to know if the subject method,
> ChIPpeakAnno::annotatePeakInBatch, can be used to determine the
> distance from each DM site to the nearest gene - as measured from the
> DM site to the nearest end of the gene, rather than the TSS of the
> gene.
> 
> Best,
> Carl Baribault
> Tulane Cancer Center