[BioC] R: how to get a list of the genes in each module in WGCNA

[Manca Marco (PATH)]

Dear Chris

you might take advantage of the rich set of tutorials that Langfelder and Horvath have made available on their WGCNA page ( http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/ )

Specifically the one entitled "Interfacing network analysis with other data such as functional annotation and gene ontology" seems to answer your needs -> http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-04-Interfacing.pdf

If you have more specific doubts/questions after exploring these documents, please do not hesitate to contact our mailing list again.

Best regards, Marco

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Dr Marco Manca
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

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Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Christopher Gregg [guest] [guest at bioconductor.org]
Inviato: mercoledì 18 gennaio 2012 23.39
A: bioconductor at r-project.org; chris.gregg at neuro.utah.edu
Oggetto: [BioC] how to get a list of the genes in each module in WGCNA

Hi,

My group has been using the WGCNA package to uncover gene modules in RNA-Seq data.  We are just starting to learn the package and it is very complex.  We have managed to generate the dendrogram that reveals the gene modules in a graphical format by following one of the vignettes.  However, we can't figure out how to write out a file of the genes that were assigned to each of the modules.  Can anyone please offer some insights on this aspect of the analysis or a vignette that takes one through these steps?

Thank you very much.

Sincerely,
Chris

 -- output of sessionInfo():

R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] annotate_1.32.0      AnnotationDbi_1.16.5 Biobase_2.14.0       DBI_0.2-5            DESeq_1.6.1
 [6] genefilter_1.36.0    geneplotter_1.32.1   grid_2.14.0          IRanges_1.12.3       RColorBrewer_1.0-5
[11] RSQLite_0.10.0       splines_2.14.0       survival_2.36-10     xtable_1.6-0

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