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

[Robert Castelo]

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
>>
>> _______________________________________________
>> 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