450k CpG methylation to functional annotation

Question

[bioklo]

Hi,

I have a list of CpGs from Illumina 450k and I would like to map the individual probes (CpGs) to specific genes/promoters/enhancer regions. Is any way to do this is R?

Thank you in advance.

-bioklo

Answer 1

[s.w.vanderlaan]

Can't you just use the annotation file from Illumina?

[bioklo]

Thanks. Do you know if is any package for annotation, or I should use the .csv file?

[Charles Warden]

I would just use the annotation files from Illumina, but there is also an annotation package in Bioconductor:

http://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html

Please see this post:

How do I get gene annotation for probes on Illumina's HM450k arrays in FDb.InfiniumMethylation.hg19?