2.8 years ago by

EMBL European Molecular Biology Laboratory

Dear Bryon

I am not sure there is "the intended method". Most of the code in this package is >10 years old, and it was contributed by several authors at the time. So, contributions and patches from you will also be welcome.

Some observations that might be useful:

`as(adj, "graphNEL")`

with `adj`

a `matrix`

proceeds via `matrix -> graphAM -> graphNEL`

(look for `setAs("matrix", "graphNEL")`

in `mat2graph.R`

), and for `setAs(from="graphAM", to="graphNEL")`

in `methods-graphAM.R.`

None of that code is set in stone, nor is it very complicated, and patches are welcome.
- There is also the function
`ftM2graphNEL`

(which internally invokes `.ftM2other`

), and this might be closer to what you need. (`ftM`

stands for 'from-to-matrix', and the design idea at the time was to implement the core functionality as normal R functions and only in a second layer wrap them into S4 methods.) The transformation from adjacency matrix to from-to-matrix is simple (essentially, `which(aM!=0, arr.ind=TRUE)`

). In any case, also that function is simple and you could modify it to your needs.
- And then there is
`aM2bpG`

, which is intended for bipartite graphs (i.e. the matrix can be non-square and is expected to have different sets of row and column names) - but there I noted a line that assumes positive edge weights, for no obvious reason, and simply replacing a `>`

operator with an `!=`

should generalize that.

Another question is whether you have to use the graph package. There are more actively maintained packages with overlapping aims (e.g. the `igraph`

package on CRAN) - which is part of the reasons why `graph`

authors have decided to maintain, but not further develop the latter.

Hope this helps

Wolfgang