I have paired RNA-seq data and WGBS data for a particular experiment with a complex design.
So far, I've performed differential expression analysis on the RNA-seq data using DESeq2 and a multiple linear regression model of this type:
Expression ~ Donor + Gender + CellType + Treatment
I would like to analyse the methylation data using the same linear model:
Methylation ~ Donor + Gender + CellType + Treatment
Are there any Bioconductor packages that allow me to fit a multiple linear regression model on WGBS data?