[Bioc-devel] annoSet?

[Martin Morgan]

On 08/12/2015 02:01 PM, Vincent Carey wrote:
> It seems to me we may need a class to manage related annotation
> structures.  For example, the chromImpute segmentations of the genome
> defined for various cell types.  I would like to be able to take a region
> of the genome (say a SNP) and ask how the state varies across cell types.
>
> AnnotationHub will provide access to cell-type specific GRanges but there
> is no container that I can think of that would coordinate these as analogous
> to different "samples".

A somewhat different strategy is to manage the cached (or in some cases remote, 
as with bigWig) files and associated ranges, along the lines of

     library(GenomicFiles)      # aarg, 'Biobase::cache & AnnotationHub::cache !
     library(AnnotationHub)
     register(SerialParam())    # turn off parallel eval for development

     hub = AnnotationHub()
     hublet = query(hub, c("files i'm", "interested in"))
     fls = cache(hublet)        # cache (if need) and return local path to files
     ## alternative, e.g., rtracklayer::bigWig supports remote query
     ## urls = hublet$sourceurls

     rngs = GRanges("chr10", IRanges(c(100000, 200000), width=1))
     gf = GenomicFiles(rngs, fls) # use this to manage

     MAP = function(rng, fl) import(BEDFile(fl), which=rng)$name
     REDUCE = unlist
     xx = reduceFiles(gf, MAP=MAP, REDUCE=REDUCE)
     mcols(rngs) = simplify2array(xx)
     ## or SummarizedExperiment(list(my=simplify2array(xx)), rowRanges=rngs)

>
> Am I missing something?
>
> 	[[alternative HTML version deleted]]
>
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