Question: edge-less pathways in graphite
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gravatar for Hamid Bolouri
7.4 years ago by
United States
Hamid Bolouri90 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="--&gt;"/> <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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ADD COMMENTlink modified 7.4 years ago by Paul Shannon750 • written 7.4 years ago by Hamid Bolouri90
Answer: edge-less pathways in graphite
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gravatar for Paul Shannon
7.4 years ago by
Paul Shannon750
Paul Shannon750 wrote:
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="--&gt;"/> > <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 > > _______________________________________________ > 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
ADD COMMENTlink written 7.4 years ago by Paul Shannon750
Thanks very much for the reality-check Paul. For compatibility reasons, I'd like to use 'graphite' graphs if I can. This isn't a show-stopper. I'll proceed without the edge-less graphs for now, and keep my fingers crossed that the missing edges will become available later. Thanks Hamid ----- Original Message ----- From: "Paul Shannon" <pshannon@fhcrc.org> To: "Hamid Bolouri" <hbolouri at="" fhcrc.org=""> Cc: "Paul Shannon" <pshannon at="" fhcrc.org="">, bioconductor at r-project.org Sent: Wednesday, April 25, 2012 12:42:57 PM Subject: Re: [BioC] edge-less pathways in graphite 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="--&gt;"/> > <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 > > _______________________________________________ > 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
ADD REPLYlink written 7.4 years ago by Hamid Bolouri90
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