CPG island annotation with gene
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5.5 years ago
kanwarjag ★ 1.1k

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

 

Thanks

 

CpG island gene annotation • 2.6k views
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5.5 years ago

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

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5.5 years ago

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

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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. 

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

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