I have read several published papers on DNA methylation prediction based on methylation patterns. However, I would like to ask if there are any existing methods for prediction on DNA methylation levels (beta values) and/or status (0 or 1) based on whole-genome sequencing data (WGS)?
I have 1,000 individuals' WGS data and DNA methylation data for only 500 out of the same1,000 individuals.
I wish to train a prediction model on 500 individuals with both WGS and DNA methylation data, and test/predict for other 500 individuals which without DNA methylation data.
Any helps are truly appreciated!
Update: I guess this preprint is highly relevant for your undertaking: MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction. Unfortunately, the web app is currently under maintenance.
Thank you very much, Matthias! I will definitely check those links out myself!