Infinium probes to Ensembl IDs

Question

[mousaedrees]

Dear Colleauges, I'm looking for an R package that has the Illumina Infinium 450K probes annotated to Ensembl IDs.

Thanks all!

Answer 1

[Hamid Ghaedi]

If I want to do this, here is the approach: using IlluminaHumanMethylation450kanno.ilmn12.hg19 to get genes (by gene symbol) , then use biomaRt to get associated ENS ID.

[mousaedrees]

Thanks a lot Hamid. Maybe also useful to note that from your hint I got to this package:

IlluminaHumanMethylationEPICanno.ilm10b4.hg19

which annotates EPIC Array, and has 2 useful columns: probes that are from 450k array, and ENST annotation. Although not all 450K array probes are in EPIC, but this covers the vast majority of them.

library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
data("Other")
450kAnn= as.data.frame(Other)
detach("package:IlluminaHumanMethylation450kanno.ilmn12.hg19", unload=TRUE)

library("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
data("Other")
EPIC= as.data.frame(Other)
EPIC= EPIC[rownames(EPIC) %in% rownames(450kAnn),]