[BioC] OSX location of bioconductor functions

[Kasper Daniel Hansen]

When you install an R package (where from source or binary), it  
installs an image so to speak of the package. You need to grab the  
source version of limma, change the toptable code inside that package  
and install it from source.

You could also try to just define a new toptable function in the  
global namespace, which would likely do what you want, since it is  
for display purposes. You can get the function definition just by
  R> toptable
and you can also dump the function to a file by
  R> dump("toptable", file = "toptable.R")
which you edit and later source.

Kasper

On Mar 8, 2007, at 3:24 PM, Bobby Prill wrote:

> Can someone tell me where toptable() code resides on an OSX
> installation?
>
> I just upgraded my R and Bioconductor.  Apparently, some rows were
> renamed in toptable().  I would like to change the row called "logFC"
> back to "M".
>
> I searched my system and can not find where any of the limma
> functions are defined.  Limma seems to be installed in:
>
> /Library/Frameworks/R.framework/Versions/2.4/Resources/library/limma/
>
> However I do not see any actual functions defined there.
>
> I installed using the command:  getBioC().  Perhaps that installed
> "binary" rather than "source" version of limma?
>
> I don't want to create a new function called my.toptable().  I just
> want all of my scripts to simply work again with a single edit of the
> true toptable().
>
> As an aside, I can't imagine why the column names in ANY function
> would be changed.  These column names are essentially the external
> interface to the function.  It seems like a very bad design decision
> to just one day change "M" to "logFC."
>
> I appreciate the help.  This is a great user community.
>
> - Bobby
>
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