[BioC] ftM2graphNEL unexpected error

[Wolfgang Huber]

Dear Dan,

did you read the error message? It says "The graph is undirected and the 
following edges are not reciprocated:  58|62, 57|62", so I assume what 
is going on is that your subsetted from-to table does not contain the 
edges in both directions. So, either you need to drop the 
edgemode="undirected" argument, or you need to include all edges in both 
directions.

Note the function "ugraph" that converts a directed graph into an 
undirected one (by loosing the directions)

Best wishes
  Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


> I have a set of 429 links (matrix ft with 'from' and 'to' nodes), a set of
> 281 nodes n, and a set of 429 link weights w.
> I wish to create graphs using subsets of the links. Sometimes this works,
> sometimes not (see below). Essentially, if too few links are included then
> the graphNEL object is not created.
> If anyone would like the data, I can email them directly.
> 
> Any help greatly appreciated.
> 
> Dan Bebber
> 
> using R 2.4.1 and graph 2.4.0
> 
> ------------------------------------------------------------------------------------------------
> 
>> ftM2graphNEL(ft[1:429,], V=n, W=w[1:429], edgemode="undirected")
> A graphNEL graph with undirected edges
> Number of Nodes = 281
> Number of Edges = 429
> 
>> ftM2graphNEL(ft[1:420,], V=n, W=w[1:420], edgemode="undirected")
> A graphNEL graph with undirected edges
> Number of Nodes = 281
> Number of Edges = 420
> 
>> ftM2graphNEL(ft[1:220,], V=n, W=w[1:220], edgemode="undirected")
> The graph is undirected and the following edges are not reciprocated:
>  58|62, 57|62
> 
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