On Wed, Jan 15, 2014 at 7:41 PM, Brett Spurrier <brett.spurrier@gmail.com>wrote:

> Hi there,
>
> I am trying to use *exomeCopy* to discover any CNVs in a particular gene
> (although analyzing the entire exome is idea).
>
> I am stepping through the R steps found in:
>
> http://bioconductor.org/packages/devel/bioc/vignettes/exomeCopy/inst/doc/exomeCopy.pdf
>
> but I get lost when I reach the line:
> counts[["GC.sq"]] <- example.counts$GC^2
>
>
the author should respond, but my guess is that this is just an error in
the vignette, as this part comes from an eval=FALSE section.

example.counts is undefined at that point in the code chunk; i think
"counts"
is intended, as counts$GC has just been defined, and this is just a
squaring and
saving of that quantity.  if you look further down in the vignette there
are executable
lines involving example.counts where this variable seems to be properly
defined



> I have no idea where example comes from? And it's referenced in later steps
> as well.
>
> Can someone help me figure out what or where the example object should come
> from?
>
> Thanks!
> Brett
>
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