Question: How To Annotate Methylation 27K?
0
gravatar for mms140130
2.5 years ago by
mms14013060
mms14013060 wrote:

Hello,

I am wondering how to map these probes to genes symbol? for methylation 27K

I have data look like this

          TCGA-A1-A0SD-01A-11D-A112-05 TCGA-A2-A04N-01A-11D-A112-05
cg00000292                   0.60555263                   0.74339575
cg00002426                   0.06197412                   0.07044132
cg00003994                   0.33345006                   0.32317983
cg00005847                   0.67217034                   0.43624235
cg00006414                           NA                           NA
cg00007981                   0.05555761                   0.05560326

or is the following is the annotation??

           Gene_Symbol Chromosome Genomic_Coordinate
cg00000292        ATP2A1         16           28890100
cg00002426         SLMAP          3           57743543
cg00003994         MEOX2          7           15725862
cg00005847         HOXD3          2          177029073
cg00006414 ZNF425;ZNF398          7          148822837
cg00007981         PANX1         11           93862594

appreciate your help, could you please show the R code from BIconductor ? I can't find it in the manual Illumina Illumina Human Methylation 27k annotation data

gene • 1.1k views
ADD COMMENTlink modified 2.5 years ago by Farshad0 • written 2.5 years ago by mms14013060

Looks like I found the solution :)

x <- IlluminaHumanMethylation27kSYMBOL
 # Get the probe identifiers that are mapped to a gene symbol
 mapped_probes <- mappedkeys(x)
 # Convert to a list
 xx <- as.list(x[mapped_probes])
 xx[1:5]
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by mms14013060
0
gravatar for Farshad
2.5 years ago by
Farshad0
Canada
Farshad0 wrote:

Thanks for your update. You forgot to say where the function should be sourced from. That is:

source("http://bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation27k.db")

For 450K kits, this package should be installed:

source("http://bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation450k.db")
ADD COMMENTlink written 2.5 years ago by Farshad0
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