This is a test version of Biostars. For the public version, visit https://www.biostars.org.
"precedence" in genomation R package

Hi everyone. I am trying to annotate CpG sites from my downstream analysis. But when using annotateWithGeneParts(), sometimes it returns more than one feature (exon, intron, promoter...) for a single methylation site. What is the purpose of this? I think a single nucleotide can only overlap in one region. When I try to draw a pie chart to visualise the proportions of the features, it allows me to prioritise the regions to get 100% in total. Otherwise it draws bar chart. Thanks in advance.

wgbs methylation array
• 742 views • link
written by Burak Özyürek • Burak Özyürek

1 answer

Because depending on how you define those regions, they can overlap, e.g. defining promoters as 1000 bp upstream and 200 bp downstream of the TSS may result in a given CpG overlapping both the promoter and an intron (or exon).

• 0 views • link
written by jared.andrews07 jared.andrews07

Log in to answer this question.

More posts like this