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how to get the file of CG sites correspond to gene about Infinium MethylationEPIC platform

I have DNA methlation data. I want get the relationship of cgXXX and gene symbol. But I don't know where to get this relationship file.

site cg gene symbol
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updated by Papyrus Papyrus • written by 924861370 • 924861370

1 answer

The "Manifest" files with that info are available at the Illumina website.

Much more easily, in R, you can retrieve them like this:

library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
anno <- as.data.frame(getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19))

To get a table with probe IDs and associated information including genes, etc. Or you can use the coordinates shown there to map to genes via other packages (e.g. ChIPseeker).

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written by Papyrus Papyrus

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