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