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

[Paul Shannon]

Hi Robert,

I just added your suggested code to the devel version of methods-graphBAM.R, along with a unit test which first reproduced the bug your found -- and which now testifies to its resolution with your fix in place.

Out of what may be an excess of caution on my part, I will wait a couple of days to see the devel build complete,  before adding your bug fix to release.  

Many thanks for helping out.  We are grateful.

 - Paul

On Jul 4, 2013, at 12:02 AM, Robert Castelo wrote:

> hi Paul, just in case it helps, the current definition of the edgeMatrix() method for 'graphBAM' is:
> 
> setMethod("edgeMatrix", "graphBAM",
>          function (object, duplicates = FALSE) {
>            bitvec <- object at edgeSet@bit_vector
>            nds <- nodes(object)
>            df <- .Call(graph_bitarray_rowColPos, bitvec)
>            t(df)
>          })
> 
> so clearly the argument 'duplicates' is not taken into account, i believe a possible fix could be the following:
> 
> setMethod("edgeMatrix", "graphBAM",
>          function(object, duplicates=FALSE) {
>            bitvec <- object at edgeSet@bit_vector
>            nds <- nodes(object)
>            df <- .Call(graph_bitarray_rowColPos, bitvec)
>            if (duplicates)
>              df <- rbind(df, cbind(as.vector(df[, "to"]),
>                          as.vector(df[, "from"])))
>            t(df)
>          })
> 
> 
> cheers,
> robert.
> 
> On 07/04/2013 04:59 AM, Paul Shannon wrote:
>> 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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>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> 
> 
> -- 
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
> 
> _______________________________________________
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