[BioC] can't get degree function to work in graph package

[Dan Tenenbaum]

Hi Burak,

On Mon, Mar 12, 2012 at 10:29 AM, Burak Kutlu <bkutlu at systemsbiology.org> wrote:
> Hello
> I am trying to call 'degree' on a graphNEL object and I get the following error using the example from the vignette.
> Thanks for your help
> -burak
>
>> library(graph)
>> set.seed(123)
>> g1 = randomEGraph(LETTERS[1:15], edges=100)
>> g1
> A graphNEL graph with undirected edges
> Number of Nodes = 15
> Number of Edges = 100
>>
>>
>> nodes(g1)
>  [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O"
>> degree(g1)
> Error in degree(g1) : Not a graph object
>>

Looks like you are hitting the degree() function in the igraph package.
Try explicitly calling:
graph::degree(g1)

Dan

>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] igraph_0.5.5-4        RBGL_1.30.1           org.Mm.eg.db_2.6.4
> [4] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.18
> [7] Biobase_2.14.0        graph_1.32.0          BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6 tools_2.14.1
>>
>        [[alternative HTML version deleted]]
>
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