[BioC] Create A Stranded probeAnno Object

[Kasper Daniel Hansen]

I could be wrong, but as far as i remember from when I used
tilingArray, the probeAnno object was just a simple list or
environment.  It was not wrapped in a classes structure at all.  I
suggest you look at the davidTiling package, which contains a
probeAnno object.  It was pretty easy to figure out how the object
should be structured.

Kasper

On Fri, May 25, 2012 at 2:15 AM, Dario Strbenac
<d.strbenac at garvan.org.au> wrote:
> Sorry, bad example for the last part. Here's what I was meant to show.
>
>> segments <- segChrom(intensRBNorm, probes, chr = c("chr9", "chr10"), strands
> = c('+', '-'), nrBasesPerSegment = 500000, maxk = 500, step = 7)
> Running 'segment' on chromosome chr9.+ ... complete
> Running 'segment' on chromosome chr9.- ... complete
> Running 'segment' on chromosome chr10.+Error in segment(ychr, maxseg = nsegs,
> maxk = maxk) :
>  maxseg must be an integer of length 1 between 1 and nrow(y)=0
>> head(probes["chr10.+.start"])
> integer(0)
>> head(probes["chr10.-.start"])
> [1] 44872512 44872538 44872560 44872588 44872612 44872634
>
> Only a few genes on chr10 - strand are tiled, none on + strand. I'll get around
> it by creating a probeAnno object for chromosomes that have both strands tiled,
> one for only +, and one for only -, and likewise for intensity matrices.
>
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