Question: 450k CpG methylation to functional annotation
0
gravatar for bioklo
4.7 years ago by
bioklo0
bioklo0 wrote:

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

sequencing R genome • 3.3k views
ADD COMMENTlink modified 4.7 years ago by s.w.vanderlaan40 • written 4.7 years ago by bioklo0
1
gravatar for s.w.vanderlaan
4.7 years ago by
Netherlands
s.w.vanderlaan40 wrote:

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

ADD COMMENTlink written 4.7 years ago by s.w.vanderlaan40

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

ADD REPLYlink written 4.7 years ago by bioklo0
1

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?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Charles Warden7.9k
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