Hi,

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?

Thank you!