Using genomation to analyze methylation profiles from Roadmap epigenomics and ENCODE

By Katarzyna Wręczycka

(This article was first published on Recipes, scripts and genomics, and kindly contributed to R-bloggers)


Distribution of covered CpGs across gene regions

genomation facilitates visualization of given locations of features aggregated by exons, introns, promoters and TSSs. To find the distribution of covered CpGs within these gene structures, we will use transcript features we previously obtained. Here is the breakdown of the code

  1. Count overlap statistics between our CpGs from WGBS and RRBS H1 cell type and gene structures
  2. Calculate percentage of CpGs overlapping with annotation
  3. plot them in a form of pie charts

To leave a comment for the author, please follow the link and comment on his blog: Recipes, scripts and genomics. offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more…

Source:: R News

Leave a Reply

Your email address will not be published. Required fields are marked *

Time limit is exhausted. Please reload CAPTCHA.