[BioC] graph::join discards node and edge attributes

[Paul Shannon]

I have two well-annotated kegg pathway graphs I wish to merge.

Using graph::join, the nodes and edges merge nicely, but all the edge and node attributes are lost, and a new edge attribute 'weight' is added.

> names (nodeDataDefaults (g.05200))  
   [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
> names (nodeDataDefaults (g.04010))  
   [1] "type"  "label" "desc"  "BP"    "MF"    "CC"    "phase" "score" "lfc"   "pval"
> names (nodeDataDefaults (g.both))   
  NULL


> names (edgeDataDefaults (g.04010))
  [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
> names (edgeDataDefaults (g.05200))
  [1] "edgeType"   "pmid"       "abstract"   "reciprocal" "score"      "source"
> names (edgeDataDefaults (g.both))
  [1] "weight"

Is there any graph method, current or planned, which will preserve node and edge attributes?  I realize that attribute conflicts can arise, and some strategy is required to handle these.

 - Paul


> sessionInfo ()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] RCytoscape_1.1.6     org.Mm.eg.db_2.4.1   RCurl_1.4-3          bitops_1.0-4.1       GOstats_2.16.0       Category_2.16.0      GO.db_2.4.5
 [8] GSEABase_1.11.2      annotate_1.28.0      KEGG.db_2.4.1        KEGGgraph_1.4.0      graph_1.26.0         XML_3.2-0            SPIA_1.8.0
[15] org.Hs.eg.db_2.4.6   RSQLite_0.9-2        DBI_0.2-5            AnnotationDbi_1.11.8 Biobase_2.10.0       RUnit_0.4.26

loaded via a namespace (and not attached):
[1] genefilter_1.32.0 RBGL_1.25.0       splines_2.12.0    survival_2.35-8   tools_2.12.0      XMLRPC_0.2-2      xtable_1.5-6