How can one extract the (smoothed) methylation values for the sites of a bump for the baseline (control group) from the output object of the bumphunting function? Have I misunderstood something or is it not possible to (directly) obtain these values?

Because my question is generic, I will post the example code from the help site of the bumphunting function.

library("bumphunter")

dat <- dummyData()

bumps <- bumphunter(dat$mat, design=dat$design, chr=dat$chr, pos=dat$pos,
                         cluster=dat$cluster, coef=2, cutoff= 0.28, nullMethod="bootstrap",
                         smooth=TRUE, B=250, verbose=TRUE,
                         smoothFunction=loessByCluster)

Fabian