InitialAlignment: Create initial alignment
In GraphAlignment: GraphAlignment

Description Usage Arguments Details Value Author(s) Examples

Create a permutation for an initial alignment. Either "random" or "reciprocal" may be specified as the mode argument.

1	InitialAlignment(psize, r=NA, mode="random")

`psize`	size of the alignment
`r`	node similarity score matrix (required for mode 'reciprocal')
`mode`	type of initial alignment

To create a random initial alignment of size psize, the InitialAlignment function can be used with the mode argument set to "random". If mode is set to "reciprocal", a reciprocal best match algorithm is applied to the input matrix R to find an initial alignment. This mode requires that the psize argument is sufficiently large to allow for the addition of dummy nodes to which unaligned nodes can formally be aligned.

The return value is a permutation vector of the specified size.

Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg

  ex<-GenerateExample(dimA=22, dimB=22, filling=.5, covariance=.6,
    symmetric=TRUE, numOrths=10, correlated=seq(1,18))
  
  pinitial<-InitialAlignment(psize=34, r=ex$r, mode="reciprocal")