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Vining, Kelly
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@vining-kelly-6557
Last seen 10.3 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.