No. of promoters in peaks / No of promoters in whole genome

YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization

https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585

214 stars 74 forks source link

No. of promoters in peaks / No of promoters in whole genome #50

Open girdhar3 opened 7 years ago

girdhar3 commented 7 years ago

Prerequisites

[ ] Have you read Feedback and follow the guide?
- [ ] make sure your are using the latest release version
- [ ] read the documents
- [ ] google your quesion/issue

Describe you issue

[ ] Make a reproducible example (e.g. 1)
[ ] your code should contain comments to describe the problem (e.g. what expected and actually happened?)

Ask in right place

[ ] for bugs or feature requests, post here (github issue)
[ ] for questions, please post to Bioconductor or Biostars with tag ChIPseeker

girdhar3 commented 7 years ago

I want to calculate percentage of promoters in my peaks as total number of promoters in whole genome. I want to do this analysis for all other annotated regions. how can I do this? I have figured out for promoters, introns, exons , 5utr, 3utr. How do you do for downstream and distal intergenic regions? to No. of promoters in peaks / No of promoters in whole genome

spooner1 commented 6 years ago

Maybe not the same, but points in the same direction... Is it possible, to add the "normal" distribution of features to "plotAnnoBar"? Then possible enrichments in regions, e.g. the Promoterregions, could be determined by this plot.