Question: How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
gravatar for hdy
5.0 years ago by
United States
hdy100 wrote:

I am dealing with methylation data and see those entries are describe as CpG/CpH coordinate (UCSC hg19, Feb 2009), like: cg00013618 and cg00027083. How can I retrieve the gene names or ids from these coordinate information?

methylation • 7.6k views
ADD COMMENTlink modified 4 months ago by RamRS20k • written 5.0 years ago by hdy100
gravatar for GANI
5.0 years ago by
United States
GANI220 wrote:

I see that based on the probe Identifiers, you were using Illumina Methylation data. What specific platform are you using (27k or 450k)? Also, what tools/language are you using to perform the analysis?

If you are working in R, you can use the following package to retrieve the corresponding gene information for 27k platform.

or the following package for 450k platform

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by GANI220

I am using 27K now but probably will also head into 450K as well, thank you for your advice and I do use R. Do you know, if I am dealing with 450k, what tools may help and give me results?

ADD REPLYlink written 5.0 years ago by hdy100

I just updated my post with the 450k annotation as well.

ADD REPLYlink written 5.0 years ago by GANI220

Here's the R-code.


CpG_annotation <- as.list(IlluminaHumanMethylation450kSYMBOL[mappedkeys(IlluminaHumanMethylation450kSYMBOL)])
ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by sjorsvanheuveln50
gravatar for Isaac Joseph
2.3 years ago by
Isaac Joseph80
Berkeley, CA USA
Isaac Joseph80 wrote:

So, for posterity, to save time and do something roughly equivalent, just do biocLite('FDb.InfiniumMethylation.hg19')instead of the above.

Details: the above appears to be deprecated; I received the following error:



    Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
      call: NULL
      error: 'fun' is defunct.
    Use 'FDb.InfiniumMethylation.hg19' instead.
    Use 'FDb.InfiniumMethylation.hg18' instead.
    Use 'mapToGenome() function in minfi or methylumi' instead.

, suggesting that I use one of these other databases.

ADD COMMENTlink written 2.3 years ago by Isaac Joseph80

Plot twist: said posterity now includes me, as I forgot how to do this, and moreover, forgot that I knew how to do this, so Google®ed it and came upon this question again.

ADD REPLYlink written 2.1 years ago by Isaac Joseph80
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe35k
Republic of Ireland
Kevin Blighe35k wrote:

Same issue here and just became really [really] tired of these annotation packages becoming outdated.

You can easily obtain the 450k methylation annotation data from Illumina's website, where it should always remain and not vanish into thin air:


ADD COMMENTlink modified 4 months ago • written 4 months ago by Kevin Blighe35k
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