[BioC] graph object question

[Vincent Carey]

as usual there are many way to proceed.  i'd suggest that you do not
try to build the edge list by hand, but start your graph with your set
of nodes

library(graph)
g = new("graphNEL", nodes = nodevec)

and then use

addEdge in the graph package to build the thing up directly as a
graphNEL instance


On Fri, Feb 12, 2010 at 5:17 PM, Iain Gallagher
<iaingallagher at btopenworld.com> wrote:
> 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
>
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