[BioC] Screeplot in puma package

[Richard Pearson]

Hi Paul

You can create one using code as in the following example:

library(pumadata)
data(pumapca_estrogen)
screePlotPoints <- apply(pumapca_estrogen at model@W, 2, function(x) sqrt(sum(x^2)))
plot(screePlotPoints)

In this example you'll see the first two components cover nearly all of the variation (as you would expect when looking at Figure 1 in the vignette).

I'll include a proper screeplot function in a forthcoming release of puma.

Hope that helps!

Richard.


Paul Geeleher wrote:
> Hi,
> 
> I'm wondering, as the subject suggests, if its possible to do a
> screeplot in puma, with the output of the pumaPCA function?
> 
> Thanks!
> 
> -Paul.
> 
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-- 
Richard D. Pearson             richard.pearson at postgrad.manchester.ac.uk
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
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