Convert Bisulfite Methylation data Genomic Position to Probes id (CpG)

Question

[ryme]

Hello,

I would like to ask if anyone has a clue on have to convert the genomic position from bisulfite methylation data to probes IDs?

For example; Converting chr1:10208081 to cg00061883.

Thanks!

Answer 1

[Basti]

If you are talking about Illumina CpG probe ID, just download EPIC/450k/27k manifest from Bioconductor and match chromosome and position.

library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
data("IlluminaHumanMethylation450kanno.ilmn12.hg19")

data(Locations)
loc450k=data.frame(Locations)

loc450k=data.frame(getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19))

library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
data("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")

data(Locations)
locEPIC=data.frame(Locations)