[BioC] Genes, their domains, and a list of superimposed mutations

[Martin Morgan]

On 08/29/2013 06:29 AM, Gabriele [guest] wrote:
>
> Dear Bioconductor mailing list,
>
> I was wondering if anyone knows whether there is any package to plot figures with a given gene, its domains, and symbols from a list of pre-specified mutations, something like what is seen in the cBio portal (http://www.cbioportal.org/public-portal/index.do) when one looks for mutations, or in COSMIC (see this example: http://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BRAF#histo )... I haven't found anything although I did my research...
>

Not a detailed answer to your question, but I'd look at Gviz (which has an 
excellent vignette) and ggbio. Martin

> Thanks!
>
>   -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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