[Bioc-devel] annoSet?

Michael Lawrence lawrence.michael at gene.com
Wed Aug 12 23:15:24 CEST 2015


Usually, I represent this with a long-form GRanges with a sample column.
But there is no formal notion of sample, and sample-level data needs to be
"denormalized".

I think you are asking for something similar to GenomicFileViews, except
for GRanges instead of files. An implementation might be a
GenomicRangesList, except the Seqinfo is coordinated across all elements.
The mcols() on the GRL would hold the phenotype data.




On Wed, Aug 12, 2015 at 2:01 PM, Vincent Carey <stvjc at channing.harvard.edu>
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".
>
> Am I missing something?
>
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