Question: How to map CpG ids to nearest genes?
0
gravatar for preethibagopi5
2.8 years ago by
preethibagopi50 wrote:

I am working in dna methylation data and I am having a .csv file containing cpg ids. I want to map the cpg sites to nearest gene. How to do that in R?

Thanks in advance

gene next-gen R genome • 2.8k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by preethibagopi50
1
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

Load the relevant txdb database and use the nearest() command, presumably with the transcripts.

ADD COMMENTlink written 2.8 years ago by Devon Ryan95k

Hi, Devon. Could you give a detail? I also have a question. When two genes are near the CpG, how to decide the nearest one. Should the TSS, promoter and gene body be considered? @Devon Ryan

ADD REPLYlink written 2.6 years ago by Kangli Wang0

Honestly it's a bit arbitrary what one considers. Biologically speaking, it'd make sense to consider genes downstream (when considering the gene's strand) or containing a SNP, but I'd have to check and see if that's possible with nearest().

ADD REPLYlink written 2.6 years ago by Devon Ryan95k
0
gravatar for nandobonf
2.8 years ago by
nandobonf0
nandobonf0 wrote:

If you are working with Illumina 450k or similar, you can use the manifest table to annotate your probes. See here: https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kmanifest.html

ADD COMMENTlink written 2.8 years ago by nandobonf0
0
gravatar for preethibagopi5
2.8 years ago by
preethibagopi50 wrote:

I try to install IlluminaHumanMethylation450k.db package for annotation but I came across this error.

Error: package or namespace load failed for 'IlluminaHumanMethylation450k.db':
 .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
  call: NULL
  error: 'fun' is defunct.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Defunct")
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/R/R-3.4.1/library/IlluminaHumanMethylation450k.db'
ADD COMMENTlink modified 2.8 years ago by Devon Ryan95k • written 2.8 years ago by preethibagopi50

Please note the "ADD COMMENT" button, which can be used to reply to specific posts.

ADD REPLYlink written 2.8 years ago by Devon Ryan95k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1369 users visited in the last hour