identify associated genes with methylation bumps

Question

[weixiaokuan]

Hi,

I have run through methylation array (illumina EPIC) pipeline using minfi or ChAMP. Now, I have obtained, DMP and DMR. I would like to annotate these locus, regions with gene information. For DMP, it's simple I just need to add gene info to each probe. However, for DMR, do you guys know a simple solution to identify all the associated genes with a DMR? I know I may write code to get those genes but if any package/function available, it will be very helpful. Thank you. -Xiaokuan

Answer 1

[igor]

There are a few packages available for annotation of regions, such as:

• ChIPpeakAnno - http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html
• ChIPseeker - http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html

[weixiaokuan]

Thank you igor. I'll give them a try. -Xiaokuan