How can I provide pair information to do pairwise differential methylation analysis?

jsh58 / DMRfinder

Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data

MIT License

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How can I provide pair information to do pairwise differential methylation analysis? #5

Closed bishwaG closed 5 years ago

bishwaG commented 6 years ago

Hi,

I have RRBS data with twin pair study design. How can I provide pair information to DMRfinder to perform pairwise differential methylation analysis?

jsh58 commented 6 years ago

Thanks for the question. The sample groups to be tested for differential methylation are specified in the call to findDMRs.r. For more details please consult the User Guide or the just-updated README, in particular the Quick start and Testing regions sections.

John Gaspar

bishwaG commented 6 years ago

Thank you @jsh58

bishwaG commented 6 years ago

Is it possible to adjust covariates in DMRfinder?

jsh58 commented 6 years ago

I do not think so, but you can check the DSS documentation to see what is possible there.

bishwaG commented 6 years ago

Hi @jsh58 It looks like it is possible to adjust covariates in DSS.