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

Question

[wangzer]

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?

Answer 1

[Devon Ryan]

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).

[wangzer]

thanks，I will try again.