transplant.RdHere we transplant a subgraph (eg representing an event) into a recipient graph. The transplant operation will (1) fix the donor ALT junction copy numbers (2) leave the subgraph node copy numbers unconstrained (3) minimize the loose ends of the resulting balanced graph
Donor and recipient graph should both have $cn field defined on nodes and edges. Donor can also just be junctions, in which case the junction shadow will be taken as the footprint, or a footprint can be manually provided. The footprint will then provide a region where the copy number constraints are relaxed while loose ends strictly enforced.
Currently transplant is only well defined for haploid / unphased graphs ie those where there is at most a single interval representing a given reference genomic regions.
transplant(gg, donor, footprint = NULL, lambda = 1000, L0 = FALSE)"haploid" gGraph with field $cn
donor (haploid) gGraph or Junction object with field $cn
if gGraph not provided then footprint can be directly provided
loose end penalty to apply to balance operation (1000) to nodes within the donor region
flag whether to use L0 penalty (FALSE)
balanced gGraph with donor junctions incorporated at their donor cn