[R] [BioC] Overlay Gene Expression on SNP (copy number) data

[Paul Shannon]

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_Jain at 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
> 
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