hi,

when I using edgeR to identify differentially methylated regions (DMR) between different groups with edgeR guidepaper, I have a question about the design matrix .

######

> sam <- rep(samples, each=2)
> meth <- factor(rep(c("Me","Un"),6), levels=c("Un","Me"))
> design <- model.matrix(~ sam + meth)
> colnames(design) <- gsub("sam","",colnames(design))
> colnames(design) <- gsub("meth","",colnames(design))
> colnames(design)[1] <- "Int"
> design <- cbind(design,
+ Me2=c(0,0,0,0,1,0,1,0,0,0,0,0),
+ Me3=c(0,0,0,0,0,0,0,0,1,0,1,0))

 The 7th column “Me” represents the methy-lation level (or M-value) in the 40-45 µm group. The 8th column “Me2” represents the differencein methylation level between the 50-55 and the 40-45 µm groups. Finally, the last column “Me3”
represents the difference in methylation level between the 60-65 and the 40-45 µm groups.

######

the contents above from edgeR guide, my question is how to to design the contrast column like 8th column.

You are probably following the edgeR methylation workflow from F1000R:

https://f1000research.com/articles/6-2055/

Since publishing that paper, we have added a new function modelMatrixMeth to edgeR to make it much easier for you. You can now simply use

design <- modelMatrixMeth(~group)

where group is your sample grouping factor. Have a look at the revised methylation workflow, which is here:

http://www.statsci.org/smyth/pubs/edgeRMethylationPreprint.pdf