Table of contents
methrix.RmdThis usage describes basic usage of the package intended to process several large bedgraph files in R. Methrix provides set of function which allows easy importing of various flavors of bedgraphs generated by methylation callers, and many downstream analysis to be performed on large matrices.
Usage is simple and involves generating a methrix object which is done with read_bedgraphs() function which, can be then passed to several other functions.
The example data analysis presented here uses the following publicly available whole genome bisulfite sequencing data from GEO: GSE90553
Ziller MJ, Ortega JA, Quinlan KA, Santos DP et al. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. Cell Stem Cell 2018 Apr 5;22(4):559-574.e9. PMID: 29551301
Here we use methrix to orchestrate WGBS analysis using best practices to our knowledge. Basic steps involved are..
- Data importing
- Intial QC and filtering steps
- DMR calling with DMR-seq
- Annotating and visualising DMRs
- Exporting methrix objects to bedGraphs and bigWigs