Genes do not have methylation levels, but you can certainly summarize the methylation around a gene (average, median, min, max; 2kb upstream, gene body, first intron). You will need to determine how best to summarize your own data, though (or if summarizing even makes sense for your questions).
As Yinzl2007, I would like to summarize the methylation level in each gene in order to correlate these values with gene expression levels in different tissues of a non-model species. I have WGBS data for four individuals of the same population, three of them at 6-7x and the fourth at a lower coverage. The gene expression profiles (obtained in a different study) comes from a different individual in the same population.
One of my doubts is whether to pool the methylomes of all the individuals to get the methylation values for each gene. I will filter out low-coverage Cs as well as for too high-coverage Cs. Do you think that this approach is adequate?
I planned of averaging the methylation percentage in each gene (approach 1), although I understand that this is a rough approach and would imply that every methylated C “weights” the same. I was considering to summarize the methylation just in the promoter region, but I wonder whether using all the methylated c's in promoter+gene body, or promoter+first intron would be a better option. Or even other alternative. I do not find any consensus on that.
Should I consider only genes containing a mínimum number of methylated C’s and discard the rest of genes? I was thinking of putting a mínimum limit of 20 Cs with a methylation level over 30%.