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Hi,
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
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