[BioC] Create A Stranded probeAnno Object

[Dario Strbenac]

> Assuming that you mean the tilingArray package, the 1st sentence of 
> Section 2 in the vignette says:
>    The function plotAlongChrom accepts an environment as its first 
> argument, which is expected to contain objects of class segmentation 
> with names given by paste(chr, c("+", "-"), sep="."), where chr is the 
> chromosome identifier.

But there is only one probeAnno class, defined in Ringo, right ? Thanks for the 
reference to the vignette, that's what I needed to know. I assumed ?probeAnno 
was the best place to find out about creating an object. My understanding is 
that vignettes are to show how the package works on real data for an analysis, 
rather than defining how to use class constructors not documented in basic help 
files.

Another aspect I found unclear was that the first two parameters to segChrom 
can be a matrix and a probeAnno object and how they were linked. Without 
reading the source code of segChrom, the user wouldn't know that the 
chrNumber.index items of a probeAnno object correspond to the row numbers/names 
of the intensity matrix. Which seems logical, but could be stated somewhere. 
I've made assumptions before about how public software works in the past, and 
it turned out it didn't work how I assumed, so I'm wary about ambiguities 
nowadays.

> However, you should feel free to do so, and you could contribute a tiling
> array package that you actually like :)

Done it once before for my package - it was an adventure ! I think I might pass 
you up on your offer.

- Dario.