[BioC] Create A Stranded probeAnno Object

[Wolfgang Huber]

Dear Dario

please can you next time be clearer which package you are refering to. 
'probeAnno' objects are defined in at least two packages: 'tilingArray' 
and 'Ringo'. (In R there is no assumption that the same class name can 
be used only by a single package in the world, this is why R has name 
spaces.)

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.

So the strand is implied by the name of the segmentation object, e.g. 
"1.+" and "1.-" correspond to the Watson and Crick stands of chromosome 
1 respectively.

Regarding the design: the tilingArray package was written in 2005, 06. 
It predates GRanges, the oligo package, and almost anything else of that 
sort. The Ringo package was written later and corrected many of the less 
streamlined aspects of the initial attempt. The IRanges-infrastructure 
was developed more recently, and is by far much more elegant and performant.

Personally, I do not see much value in refactoring the old tiling array 
code from the middle of last decade, when most people in the meanwhile 
have moved on to high-throughput sequencing, and the those who still use 
tiling arrays normally have lots of legacy code. However, you should 
feel free to do so, and you could contribute a tiling array package that 
you actually like :)

	Best wishes
	Wolfgang



May/23/12 11:00 AM, Dario Strbenac scripsit::
> Hello,
>
> I've read the help page and the vignette and I want to have the
> strand information of the probes used, but I can't see what the
> required format of the names of the vectors is. Can anyone provide a
> small example of how it's done ? It would be nice if there was a
> simple way to do this based on a data.frame or GRanges object of
> probe information, rather than having having to create lots of
> specially named vectors and mess around with environments. Also, the
> chr argument to segChrom has to be an integer vector, which means X
> and Y for human have to be artificially renamed as 23 and 24. The
> design could be more streamlined.
>
> - Dario.
>
> -------------------------------------- Dario Strbenac Research
> Assistant Cancer Epigenetics Garvan Institute of Medical Research
> Darlinghurst NSW 2010 Australia
>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber