[R] smoothScatter and geneplotter

[p_connolly at slingshot.co.nz]

On Tue, 18-Dec-2007 at 11:21AM -0500, James W. MacDonald wrote:

|> Duncan Murdoch wrote:
|> > Yes, I agree.  (As an aside, there's actually a capital S in
|> > smoothScatter(), and it's a bit of a pain to install, because
|> > geneplotter depends on something that depends on DBI, which is not so
|> > easily available these days.)
|>
|> Somehow I always forget the capital S and wonder if I have loaded the
|> correct package ;-D

Maybe you're misled from the output when the package is installed:


 >>> Building/Updating help pages for package 'geneplotter'
     Formats: text html latex example
  GetColor                          text    html    latex   example
  Makesense                         text    html    latex   example
  alongChrom                        text    html    latex   example
  amplicon.plot                     text    html    latex   example
  cColor                            text    html    latex   example

[...]

  multiecdf                         text    html    latex   example
  openHtmlPage                      text    html    latex   example
  panel.smoothScatter               text    html    latex   example
  plotChr                           text    html    latex   example
  plotExpressionGraph               text    html    latex   example
  savepng                           text    html    latex   example
  smoothscatter                     text    html    latex   example
** building package indices ...
* DONE (geneplotter)

Notice that the panel function has a capital S in its name but not the
basic function.  Does that point to a slight bug somewhere?  Could it
produce a more serious problem?


|>
|> As for installing the required dependencies, I believe this is actually
|> quite straightforward:
|>
|> source("http://www.bioconductor.org/biocLite.R")
|> biocLite("geneplotter")
|>
|> Should install geneplotter and all required dependencies.

That was about as easy as it would be possible to make it.  Thank you
for that.

best

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