[BioC] makeAttr() missing in KEGGgraph

[Martin Morgan]

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.nutrigenomicsconsortium.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