[BioC] graph::edgeMatrix() fails for signature(object="graphBAM")

[Paul Shannon]

Hi Robert,

Thanks for your clear bug report.  I will take a look at this over the upcoming weekend.

 - Paul

On Jul 3, 2013, at 7:17 AM, Robert Castelo wrote:

> hi,
> 
> i have come across the following problem with the graph::edgeMatrix() function when the input object is a 'graphBAM' object:
> 
> library(graph)
> g <- graphBAM(data.frame(from="1", to="2", weight=1))
> 
> edgeMatrix(g, duplicates=FALSE)
>     [,1]
> from    1
> to      2
> edgeMatrix(g, duplicates=TRUE) ## here is the problem !!
>     [,1]
> from    1
> to      2
> edgeMatrix(as(g, "graphNEL"), duplicates=TRUE) ## but here works !!
>     [,1] [,2]
> from    1    2
> to      2    1
> 
> 
> note that when coercing 'g' to a 'graphNEL' object, then it works as expected.
> 
> 
> thanks!!
> robert.
> ps: sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
> [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
> [7] LC_PAPER=C                LC_NAME=C
> [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] graph_1.38.2   vimcom_0.9-8   setwidth_1.0-3 colorout_1.0-0
> 
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.6.0 parallel_3.0.0     stats4_3.0.0       tools_3.0.0
> 
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