Question: Infinium probes to Ensembl IDs
0
gravatar for mousaedrees
7 weeks ago by
mousaedrees0 wrote:

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

Thanks all!

R • 129 views
ADD COMMENTlink written 7 weeks ago by mousaedrees0
1
gravatar for Hamid Ghaedi
7 weeks ago by
Hamid Ghaedi770
Canada
Hamid Ghaedi770 wrote:

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.

ADD COMMENTlink written 7 weeks ago by Hamid Ghaedi770

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),]
ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by mousaedrees0
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