This is a test version of Biostars. For the public version, visit https://www.biostars.org.
CG Target IDS from Illumina 450k

Hello All:

I have a list of CG target IDs that I have gotten from running dMPFinder. I was wondering if anyone knows of any tools or R packages that I can run in order to find the chromosome and coordinates. I know I can find them individually on UCSC Genome Browser, but I have a long list. Thank you in advance.

Sincerely, Ron

cg gene coordinates illumina 450k
• 4,188 views • link
updated by mastal511 mastal511 • written by questionaire • questionaire

1 answer

Try the R/Bioconductor package IlluminaHumanMethylation450kanno.ilmn12.hg19.

• 0 views • link
written by mastal511 mastal511

Getting the data into a standard data frame wasn't immediately obvious to me, so I thought I'd pass along the commands to help others in a similar situation:

library("IlluminaHumanMethylation450kanno.ilmn12.hg19")
data("IlluminaHumanMethylation450kanno.ilmn12.hg19")
annotation.table = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

Same idea applies to EPIC annotations:

library("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
data("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
annotation.table = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)
• 0 views • link
written by Charles Warden Charles Warden

Log in to answer this question.

More posts like this