[BioC] can't get degree function to work in graph package
pshannon at fhcrc.org
Wed Mar 14 04:59:00 CET 2012
You turned up a very odd bug. And a mysterious one.
I just looked at the unit tests for degree, and they do not include exactly the case you used: a graphNEL returned by the randomEGraph method. But degree is successfully called on graphNEL's, and those tests run every day. Puzzling.
Could you send me your g1 as an RData object?
On Mar 12, 2012, at 10:29 AM, Burak Kutlu wrote:
> 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
>> g1 = randomEGraph(LETTERS[1:15], edges=100)
> A graphNEL graph with undirected edges
> Number of Nodes = 15
> Number of Edges = 100
>  "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O"
> Error in degree(g1) : Not a graph object
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  igraph_0.5.5-4 RBGL_1.30.1 org.Mm.eg.db_2.6.4
>  RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.18
>  Biobase_2.14.0 graph_1.32.0 BiocInstaller_1.2.1
> loaded via a namespace (and not attached):
>  IRanges_1.12.6 tools_2.14.1
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