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How to quantify the DNA methylation level of a gene from WGBS data?

I have got the WGBS data and the methylation the ratio of the all sites. But I want to know the every genes' methylation level. How to quantify the DNA methylation level of a gene from WGBS data? Finally, I want plot a fig. like this. What tools can I use to implement it?

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r dna-methylation
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updated by Ram Ram • written by wangzer • wangzer

1 answer

Genes don't really have a methylation level, what you're plotting is the average of the CpG methyation in a gene. So load your data, calculate that and then plot it. You can do all of that in R (probably with GenomicRanges to make life easier).

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written by Devon Ryan Devon Ryan

thanks，I will try again.

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written by wangzer • wangzer

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