I'm interested in the significance testing performed by bumphunter. Namely, as of now bumphunter outputs two different pvalues: 1) p.value along with the fwer and 2) p.valueArea along with the fwerArea.
My understanding is that these are derived from bootstraping set at B (i.e. B=10000 for my case).
The issues is that for the region we are finding there is no agreement between the fwer or the fwer Area using a cut off of P<0.05 for the fwer: See below:
> head(dmr.pick.tops) chr start end value area cluster indexStart indexEnd fwerArea chr1 205818956 205819492 -0.06205978 0.3723587 14664 33501 33506 6 > head(dmr.pick.tops)”continued” L clusterL p.value fwer p.valueArea fwerArea 6 9 5.884939e-06 0.021 0.0001457223 0.41
Any advice on how to proceed or what significance value to report?