Question: CPG island annotation with gene
1
gravatar for kanwarjag
4.7 years ago by
kanwarjag1.0k
United States
kanwarjag1.0k wrote:

I have a list of CpG islands which are differential methylated. How can I get gene annotation for these island coordinates.

 

Thanks

 

cpg island annotation gene • 2.3k views
ADD COMMENTlink modified 4.6 years ago by Antonio R. Franco4.5k • written 4.7 years ago by kanwarjag1.0k
0
gravatar for andrew.j.skelton73
4.6 years ago by
London
andrew.j.skelton735.9k wrote:

What package are you using to do this analysis? If it's minfi, there's getAnnotation() function. This imports the IlluminaHumanMethylation450kmanifest package for annotation. 

ADD COMMENTlink written 4.6 years ago by andrew.j.skelton735.9k
0
gravatar for Antonio R. Franco
4.6 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

and what to do when you are not dealing with human sequences ?

ADD COMMENTlink written 4.6 years ago by Antonio R. Franco4.5k

Are you referencing my answer? OP has not specified the platform that they're using. I've made the assumption that they're referencing the Illumina Infinitum HumanMethylation450K assay, as it's the most commonly used for methylation microarrays, and Illumina don't offer this for anything other than human (as far as I'm aware). OP could be referencing bisulphite sequencing, in which case, the input for some test methods takes an iRange object. An iRange object could be made for the given species. 

ADD REPLYlink written 4.6 years ago by andrew.j.skelton735.9k

I am using bisulfite seq. and has differently methylated CpG islands which I want to map to gene. it is mm10 based 

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by kanwarjag1.0k
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