The man page for runCompareComplex:
 Details needs some filling in. I don't thing I understand what byWhich
 does.

 - the Value part - I think it should say that you return a list with
 these components

---This is done. TC

 - I don't think we want a toBeRm slot, that is a decision that should be
  left to the user

---When the interactome is build, should the merging of 2 sub-interactomes be forced to delete redundant protein complexes? toBeRm is the slot for which mergeBGMat depends on to get rid of this redundancy.

 - and I get:
 names(cc)
[1] "JC"           "maxIntersect" "equal"        "toBeRm"       "subcomplex" 
 so I think simInd needs to go away and JC and maxIntersect need to be
 documented.

the simInd and JC are the same (in the future, if there are other similarity indices, we can have people chose what they want). I will make sure that only one is there and documented.
