how to get the file of CG sites correspond to gene about Infinium MethylationEPIC platform
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14 months ago
924861370 • 0

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 • 490 views
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14 months ago
Papyrus ★ 2.2k

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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