[BioC] edge-less pathways in graphite
Paul Shannon
pshannon at fhcrc.org
Wed Apr 25 21:42:57 CEST 2012
Hello Hamid,
Thanks for the report.
As a sanity check, I just ran some code using Jitao David Zhang's KEGGgraph package. It retrieves a graph with what appears to have a full set of edges:
library (KEGGgraph)
library (KEGG.db)
tbl.kp = toTable (KEGGPATHID2NAME)
kegg.id.erbB = tbl.kp [grep ('erbb', tbl.kp$path_name,ignore=T),]$path_id
temp.file = 'erbB.download'
retrieveKGML (kegg.id.erbB, organism='hsa', destfile=temp.file, method='internal')
tbl.erbB = parseKGML2DataFrame (temp.file)
g.erbB = parseKGML2Graph (temp.file, expandGenes=TRUE)
head (tbl.erbB)
from to subtype
1 hsa:2885 hsa:6654 activation
2 hsa:2885 hsa:6655 activation
3 hsa:2885 hsa:2549 activation
4 hsa:2066 hsa:6776 activation
5 hsa:2066 hsa:6776 phosphorylation
6 hsa:2066 hsa:6777 activation
g.erbB
A graphNEL graph with directed edges
Number of Nodes = 87
Number of Edges = 214
Knowing now that the full graph CAN be retrieved, I will look into graphite, see what we can figure out.
- Paul
On Apr 25, 2012, at 11:03 AM, Hamid Bolouri wrote:
> hi; I am finding that some KEGG pathway graphNELs generated by graphite have zero edges, even though the KGML description includes edges, e.g.
>
>> kegg[["ErbB signaling pathway"]]
> "ErbB signaling pathway" pathway from KEGG
> Number of nodes = 87
> Number of edges = 0
> Type of identifiers = native
> Retrieved on = 2011-05-05
>
> Whereas the KGML for the same pathway includes statements such as:
>
> <relation entry1="75" entry2="46" type="PPrel">
> <subtype name="activation" value="-->"/>
> <subtype name="phosphorylation" value="+p"/>
> </relation>
>
> Am I missing something?
>
> Thanks for a great package, BTW!
>
> Hamid Bolouri
> PS Of the 46 apparently edge-less graphite graphNELs, several have zero edges in KEGG also, e.g. kegg[["Spliceosome"]]. I am _not_ talking about those.
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] graphite_1.2.0 AnnotationDbi_1.18.0 Biobase_2.16.0
> [4] BiocGenerics_0.2.0 RSQLite_0.11.1 DBI_0.2-5
> [7] graph_1.34.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.2 org.Hs.eg.db_2.7.1 stats4_2.15.0 tools_2.15.0
>
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