How to change CpG methylation cutoffs in edgeR

Question

[embueno]

Hi everyone,

I’m using edgeR to analyze a WGBS dataset using a glm. I’m working with an invertebrate genome with very low levels of CpG methylation in the genome (~3%) and want to change the cutoff for percent the CpG methylation for my samples (methylated Cs sample A/coverage for sample A) *100 and then filter them so that at least one sample with 20% methylation or more are included in the analysis. Any ideas on how to implement this edgeR would be appreciated!

[iraia.munoa]

Hi! I have a question about what edgeR manual or pipeline do you use to obtain the results in methylation % format and not in Fold Change as it is tipical for edgeR Thanks!