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Same issue here and just became really [really] tired of these annotation packages becoming outdated.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