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

[Robert Castelo]

hi Paul,

the devel version seems to build smoothly, could you push the fix to 
release?

thanks!
robert.

On 07/08/2013 06:30 AM, Paul Shannon wrote:
> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> 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