Hello, The KEGGgraph vignette depicts an example in which the command "makeAttr" is regularly used. However, this command is simply not available! Not in KEGGgraph and a search does not provide anything. So my question is: does somebody know how I am supposed to access the makeAttr function? > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] org.Hs.eg.db_2.4.1 RSQLite_0.8-4 DBI_0.2-5 [4] AnnotationDbi_1.10.0 Biobase_2.8.0 KEGGgraph_1.4.0 [7] Rgraphviz_1.26.0 graph_1.26.0 XML_2.8-1 loaded via a namespace (and not attached): [1] tools_2.11.0 Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl<mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl<http: www.nutrigenomi="" csconsortium.nl=""/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/

On 05/26/2010 05:06 AM, Groot, Philip de wrote: > Hello, > > The KEGGgraph vignette depicts an example in which the command > "makeAttr" is regularly used. However, this command is simply not > available! Not in KEGGgraph and a search does not provide anything. > So my question is: does somebody know how I am supposed to access the > makeAttr function? try browseVignettes('KEGGgraph') and view the R script associated with the vignette you're interested in. I think you'll see that it's defined elsewhere in the vignette (and that you can 'source()' the R script into your R session and verify that it is in fact executed when the PDF is vignette is processed). The information is also available from bioconductor.org -> Software -> KEGGgraph, leading to http://bioconductor.org/packages/2.6/bioc/html/KEGGgraph.html Martin >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > other attached packages: > [1] org.Hs.eg.db_2.4.1 RSQLite_0.8-4 DBI_0.2-5 > [4] AnnotationDbi_1.10.0 Biobase_2.8.0 KEGGgraph_1.4.0 > [7] Rgraphviz_1.26.0 graph_1.26.0 XML_2.8-1 > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Regards, > > Dr. Philip de Groot Ph.D. > Bioinformatics Researcher > > Wageningen University / TIFN > Nutrigenomics Consortium > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > PO Box 8129, 6700 EV Wageningen > Visiting Address: Erfelijkheidsleer: De Valk, Building 304 > Dreijenweg 2, 6703 HA Wageningen > Room: 0052a > T: +31-317-485786 > F: +31-317-483342 > E-mail: Philip.deGroot at wur.nl<mailto:philip.degroot at="" wur.nl=""> > Internet: http://www.nutrigenomicsconsortium.nl<http: www.nutrigeno="" micsconsortium.nl=""/> > http://humannutrition.wur.nl/ > https://madmax.bioinformatics.nl/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793