[Bioc-devel] efficient use of edgeData (graph)

Paul Shannon pshannon at systemsbiology.org
Wed Nov 10 21:13:55 CET 2010

Hi Nishant,

Thank you!

I misconstrued the arguments.  Seeing that 'from' and 'to' were obligatory arguments, I assumed there was no way to attain the moral equivalent of

    edgeData (graph, attr='some attribute')

Based on your reply, and a quick look at showMethods ('edgeData') I see that the 'from' and 'to' arguments default to 'missing', giving me exactly what I want, with a startling increase in speed on my 9000-edge graph.


 - Paul

On Nov 10, 2010, at 11:20 AM, Nishant Gopalakrishnan wrote:

> Hi Paul,
> Why not directly use the edgeData function with the attribute name you
> want instead of having to retrieve the edgeData for all the attributes
> and then subsetting.
> ie   edgeData(graph, from  , to , attr = edge.attribute.name)
> Nishant
> On 11/10/2010 07:01 AM, Paul Shannon wrote:
>> In the RCytoscape package I have a convenience function which returns the values of a specified edge attribute, for all edges in the graph.  It is ponderously slow on a graph of 9000 edges.
>> I define it this way:
>> function (graph, edge.attribute.name) {
>>  unlist (sapply (names (edgeData (graph)), function (n) edgeData (graph)[[n]][[edge.attribute.name]]))
>>  }
>> Can anyone suggest ways to speed this up?   I fear I am missing something obvious.
>> Thanks!
>> - Paul
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
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