Parameterizing methylKit

Steven ran a methylKit parameterization R script for me on klone. I’m (finally) following up on some of the comments and output!

Evaluating methylKit output

The first thing I wanted to do was determine which meth.diff and min.per.group parameters provided the best balance between a conservative DML estimate and providing DML to analyze. Steven said the output from the script could be found in this folder. However, there was only output for the ploidy DML for min.per.group 9 through 12! I’m missing information for min.per.group = 8, and I’m not sure why there isn’t any pH output. I posted a comment in the same issue.

Going forward

1. Continue parameter testing for DML identification
2. Revise methylKit methods and results
3. methylKIt randomization test
4. ATAC-Seq data integration
5. KOG-MWU for Crassostrea methylation comparison
6. Revise discussion
7. Revise introduction
8. Transfer scripts used to a nextflow workflow