On Mon, Apr 20, 2009 at 11:19 AM, <ig2ar-saf2@yahoo.co.uk> wrote:

>
> Hello fellow listers,
>
> Is there a document summarizing the myriad of data containing classes?
>

No, not yet. We're working on a vignette for the IRanges package (we'll have
something in about a week), which will need to be complemented by additional
vignettes in Biostrings and BSgenome. There is probably also a need for a
high-level vignette explaining the sequence infrastructure in BioC.


>
> I am trying to find a map to help me understand what is the difference
> between, say, GenomicData, GenomeData, GenomedataList, etc.
>
> I need to be able to inter-convert data, merge different sources of data,
> and also subset data.
>

Can you be more specific? GenomicData is no longer a class, but there is a
GenomicData function, which is a genome-oriented constructor for RangedData
in the rtracklayer package. GenomeData (from the BSgenome package) is for
storing arbitrary data objects on a per chromosome level. RangedData (in
IRanges) is similar, except the data need to fit into a rectangular
data.frame-like structure.

Hope this helps and sorry for the confusion,
Michael


>
> For a single class, I think that finding the information is easy. For many
> classes, it gets challenging.
>
> A possible solution is reading the whole BioC documentation but then BioC
> rises a productivity issue for users that are not developers.
>
> Anybody can advice?
>
> Thank you,
>
> Ivan
>
>
>
>
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