I used runDNAcopy and then merged states to give me my seglist object: 

> class(dat)
[1] "SegList"
attr(,"package")
[1] "snapCGH"
> ls(dat)
[1] "genes"       "method"      "M.observed"  "M.predicted" "num.states"  "state"
>

It plots the graphs fine, with segmentation lines and all. What I woudl like though is  a summary table of the sample and exact locations of calls. Should be easy enough to do as this data is in the plots.