Entering edit mode
Markus Schmidberger
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380
@markus-schmidberger-2240
Last seen 10.1 years ago
Hi,
I found the KEGGgraph package in the development repository. It sounds
great. But it is not working. There are no edges in the graphs!
What is wrong?
> library(KEGGgraph)
> tmp <- tempfile()
> retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget",
quiet=FALSE)
--08:58:59--
ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04110.xml
=> `/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869'
Aufl?sen des Hostnamen ?ftp.genome.jp? 133.103.100.184
Verbindungsaufbau zu ftp.genome.jp|133.103.100.184|:21... verbunden.
Anmelden als anonymous ... Angemeldet!
==> SYST ... fertig. ==> PWD ... fertig.
==> TYPE I ... fertig. ==> CWD /pub/kegg/xml/organisms/hsa ...
fertig.
==> PASV ... fertig. ==> RETR hsa04110.xml ... fertig.
L?nge: 27.902 (27K) (unma?geblich)
100%[==============================================================>]
27.902 29.55K/s
08:59:04 (29.51 KB/s) - ?/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869?
gespeichert [27902]
> file.rename(tmp, paste(tmp,".xml",sep=""))
[1] TRUE
> tmp <- paste(tmp,".xml",sep="")
> kegg <- parseKGML2Graph(tmp, expandGenes=T, genesOnly=T )
Fehler in subGraphByNodeType(gR, "gene") :
No 'gene' type found in the file, maybe it is a map file. Please try
parsing the file with 'genesOnly=FALSE'
> parseKGML(tmp)
KEGG Pathway
[ Title ]: Cell cycle
[ Name ]: path:hsa04110
[ Organism ]: hsa
[ Number ] :04110
[ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04110.gif
[ Link ] :http://www.genome.jp/dbget-bin/show_pathway?hsa04110
------------------------------------------------------------
Statistics:
99 node(s)
0 edge(s)
0 reaction(s)
------------------------------------------------------------
>
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_
DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC
_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDEN
TIFICATION=C
attached base packages:
[1] splines grid tools stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] org.Hs.eg.db_2.2.6 KEGGgraph_0.8.16 XML_1.98-1
[4] hgu133acdf_2.3.0 vsn_3.8.0 limma_2.16.2
[7] lattice_0.17-15 GeneNet_1.2.3 fdrtool_1.2.5
[10] longitudinal_1.1.4 corpcor_1.5.2 genefilter_1.22.0
[13] survival_2.34-1 hgu133a.db_2.2.5 RSQLite_0.7-1
[16] DBI_0.2-4 AnnotationDbi_1.4.0 pcalg_0.1-7
[19] mnormt_1.3-2 ggm_1.0.2 Rgraphviz_1.20.0
[22] robustbase_0.4-5 graph_1.19.6 MASS_7.2-44
[25] affy_1.20.0 Biobase_2.2.0
loaded via a namespace (and not attached):
[1] affyio_1.10.1 annotate_1.20.0 cluster_1.11.11
[4] preprocessCore_1.4.0
Thanks
Markus
--
Dipl.-Tech. Math. Markus Schmidberger
Ludwig-Maximilians-Universit?t M?nchen
IBE - Institut f?r medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://www.ibe.med.uni-muenchen.de
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4497