Overlaps with methylKit gene background

The next big step in the C. virginica project is to conduct a gene enrichment (if necessary…we’ll get to this later). I started this notebook with that intention. Before I could get into gene enrichment or description, I needed to characterize overlaps between the gene background used in methylKit and various genome feature files. I started this small analysis in December, but didn’t follow through because I was focusing on my MEPS resubmission.

The gene background from methylKit is formed using unite. I took this background and saved it as a BEDfile in this R Markdown file. I used intersectBed to find the overlaps between the gene background, exons, introns, mRNA coding regions, and transposable elements. Finally, I calculated the overlap proportions. My next step is to use these overlap proportions, and overlap proportions from DML and DMR to conduct a proportion test.

Going forward

1. Conduct a proportion test with gene background and DML/DMR overlaps with genome feature files
2. See how min_cov, alignment stringency, or SNPs affect clustering
3. Determine if a formal gene enrichment is necessary
4. If necessary, select the most appropriate gene enrichment method
5. Describe functions of most interesting genes with DML and DMR