How to retrieve the (smoothed) baseline values from the bumphunting output object?
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@fabianschroeder-9657
Last seen 6.3 years ago

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

bumphunter • 709 views