Hello,
I'm knew to methylation analysis. I started my analysis by using bismark and then continuing with methylkit. I was able to anotate my DMRs, through genomation using annotateWithFeatures. I have the percentage of target elements overlapping with features and vice versa
myinterestCpG summary of target set annotation with feature annotation:
Rows in target set: 37319
percentage of target elements overlapping with features: 2kb_downstream 2kb_upstream exon five_prime_UTR intron 23.45 24.14 15.83 0.01 11.59 three_prime_UTR 0.00
percentage of feature elements overlapping with target: 2kb_downstream 2kb_upstream exon five_prime_UTR intron 10.62 10.66 4.86 8.89 4.86 three_prime_UTR 0.00
but I wanted to plot the methylation averages along each feature. Along 2kp_upstream| gene body |2kb downstream. I understood from some of the articles that I have to divide the regions in 10 bins for example, but I don't know from where to start. Which methylkit output should I use, do you know any workflow or code that could help me?
What I am looking for is something like Figure 1-e https://www.nature.com/articles/s42003-020-1059-1/figures/1
Best regards
