Analysis: Binary clustering of R-loop regions and genomic annotations

[millerh1]

Need to perform analysis doing a binary clustering of R-loop regions and genomic annotations.

Approach will involve using the {{ RLHub }} package and the rlregions_annot() table. Outcomes should be:

• [ ] Binary membership matrix [ij] for RLRegion[i] in Annotation[j]
• [ ] Binary clustering on this matrix
• [ ] Analysis of number of clusters and parameter used
• [ ] A heatmap showing the clustering prepared with either {{ pheatmap }} or {{ ComplexHeatmap }}
• [ ] An RMarkdown notebook showing the results of the analysis -- the process of doing each database should be automated

Special Consideration regarding databases and types: We have 16m+ annotations from 693 UCSC tables. That's a lot of data -- and not all of it is equally important to us. So a good way to start might be to do one database at a time and set up an automated way to process it -- and then you can automate presenting the results in the notebook using child documents.

[millerh1]

I really like the way they did it in this paper: https://www.sciencedirect.com/science/article/pii/S2211124720308512

I think we should consider adopting a similar state approach