Another possibility for visual display of several kinds of data is RCytoscape, for which an example can be seen here:
http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/subnet.TCGA.02.0014.png This portrays 1) gene expression (green: under-expression; red: over-expression) 2) copy number (blue: high, black: low) 3) gene type (node shape: hexagons are kinases, arrows are ligands, diamonds are receptors, circles for everything else) 4) mutation status (not SNPs, but non-synonymous amino acid substitutions) 5) in the context of gene relationships, from KEGG A vignette for a larger version of this network is nearly complete. The Cytoscape network map is created from data and R code. - Paul On Apr 23, 2012, at 5:15 AM, Steve Lianoglou wrote: > Hi, > > On Mon, Apr 23, 2012 at 7:33 AM, Ekta Jain <ekta_j...@jubilantbiosys.com> > wrote: >> Hello, >> Can anyone please suggest any packages in R that can be used to overlay gene >> expression data on SNP (affymetrix) copy number ? > > I guess you mean visually? If so, I'd suggest skimming through the > vignettes of the following packages to see which one might suit you > best: > > * Gviz > * ggbio > * GenomeGraphs > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > bioconduc...@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
