GraphAlignment (version 1.36.0)

InitialAlignment: Create initial alignment

Description

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

Usage

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

Arguments

psize

size of the alignment

r

node similarity score matrix (required for mode 'reciprocal')

mode

type of initial alignment

Value

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

Details

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.

Examples

  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")