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Vining, Kelly ▴ 10@vining-kelly-6557
Last seen 7.3 years ago
Hello, I am using the MEDIPS package to find differentially-methylated regions among three developmental stages, following the vignette, and have a question about how differential coverage us calculated. The differential coverage step, from the vignette: > mr.edgeR = MEDIPS.meth(MSet1 = DE_MeDIP, MSet2 = hESCs_MeDIP, + CSet = CS, ISet1 = DE_Input, ISet2 = hESCs_Input, p.adj = "bonferroni", + diff.method = "edgeR", prob.method = "poisson", MeDIP = T, + CNV = F, type = "rpkm", minRowSum = 1) Here, CSet is "coupling set", which is used for CpG-dependent normalization of the MEDIPS SETs. For my own run, I have designated a CSet, and have an Input comparator. What I am unsure about is whether, at this step, cytosine context is being taken into account. It doesn't look like it matters whether cytosines are in CG context or not, but since MEDIPS appears to have been designed specifically for human cancer studies, and my MeDIP samples are from plants, where cytosines in all contexts can be differentially methylated, I want to make sure that I'm not losing data at this step in the analysis. Thanks for help, --Kelly V.