[BioC] graph object question

[Iain Gallagher]

Hello list

I'm trying to build graph objects showing the relationship between miRNA and genes. Is there a quick way to do this from a dataframe (see toy code below)?
When building my graph object I can't think my way through getting the 'edges' list name into my list of edges (see below)!


> testData
     symbol mirbase_id
6    2'-PDE hsa-let-7b
86    A2BP1 hsa-let-7b
331    AAK1 hsa-let-7b
1003  ABCB9 hsa-let-7b
1071 ABCC10 hsa-let-7b
1195  ABCC5 hsa-let-7b
3520  ACSL6 hsa-let-7b
3583  ACTA1 hsa-let-7b
4102  ACTR2 hsa-let-7b
4480 ACVR1B hsa-let-7b

t2<-as.list(testData[,2],)
names(t2)<-testData[,1]
nodes<-testData[,1]

for (i in 1:length(t2)) t2[[i]] <- c(names(t2[i]), t2[[i]])

> t2
$`2'-PDE`
[1] "2'-PDE"     "hsa-let-7b"
...

But what I need is...

> t2
$`2'-PDE`
$`2'-PDE`$edges
[1] "2'-PDE"     "hsa-let-7b"
...

Thanks for any help.

Iain

> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] RColorBrewer_1.0-2 Rgraphviz_1.24.0   graph_1.24.1      

loaded via a namespace (and not attached):
[1] tools_2.10.1