All answers are helpful. Tim I agree that the uncertainty of the state assignments should be readily available in principle. Michael/Martin, bridging to the AnnotationHub via GenomicFiles concepts makes sense. I am not sure we need new infrastructure at the moment.
On Wed, Aug 12, 2015 at 6:22 PM, Martin Morgan <[email protected]> wrote: > 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]] >> >> _______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
