On Mon, Apr 23, 2012 at 6:33 AM, Ekta Jain <Ekta_Jain@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 ?
>
Hi Ekta,

If you mean visually, as Steve suggested, you could try packages like
ggbio, Gviz, Rcytoscape.. it depends on how you plan to visualize your
data, track-based? circular view? net work? and what format your data are?

for example, in ggbio, it depends on what data you are using, you can
arrange your data into GRanges manually or just provide data  that
rtracklayer supported like bed, then just use autoplot, it accepts
different objects, like GRanges, IRanges, bamfiles or character... allow
some transformation like coverage. For files like bed, it automatically use
bar to represent your data and use score as y(you can specify other y).
Function tracks() allow you to bind or overlay any graphics produced by
ggbio or ggplot2, so you could work from data.frame too, it will help you
align your plots after the graphics are produced. For genomic structure, if
you want to overlay with your data, try autoplot, TranscriptDb. And if you
want to show interaction between genes, you could try either arches in
linear view or links in circular view(layout_circle).

http://tengfei.github.com/ggbio/

this website is still under development, just to show some possible cases,
it will be re-built against R 2.15 and more case studies are coming.

HTH

Tengfei



>
> Thanks,
> Ekta
> Senior Research Associate
> Bioinformatics Department
> Jubilant Biosys Pvt Ltd,
> #96, Industrial Suburb, 2nd Stage
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-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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