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BiSeq - How to handle covariates?



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  • BiSeq - How to handle covariates?


    I am attempting to use BiSeq (Hebestreit et al. 2013) to delineate DMRs among treatment groups in Bismark aligned RRBS data

    I have made a successful preliminary run through of the BiSeq workflow using my data but now I would like account for the effects of a covariate on DMR identification. BiSeq can apparently be made to work with covariates but I can't find any advice in the user guide as to how to go about doing this

    I have tried modifying the betaRegression() formula parameter to take into account metadata (where the covariate values are stored) as a covariate:

    RSbetaResults <- betaRegression(formula = ~group + metadata,
    link = "probit",
    object = RSpredictedMeth,
    type = "BR")

    Unfortunately, this did not work

    Any suggestions/advice would be gratefully received

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