Ok. That's the obsolete data structure from the chipseq package. If you look
at the Rnw for the chipseq vignette, you'll find code for converting one of
those into a GRanges, which is now the preferred way of storing that
information. I have no recollection of a coerce method from that structure
to a RangedData, though one may have existed at some point years ago.

Michael

On Mon, Oct 18, 2010 at 8:05 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Here is a string representation :
>
> > str(rs)
> Formal class 'GenomeData' [package "BSgenome"] with 4 slots
>  ..@ listData       :List of 25
>  .. ..$ chr1 :List of 2
>  .. .. ..$ -: int [1:375671] 184 191 194 507 511 522 526 545 551 562 ...
>  .. .. ..$ +: int [1:376001] 152 234 244 248 277 440 450 451 452 458 ...
>  .. ..$ chr2 :List of 2
>  .. .. ..$ -: int [1:331924] 384 392 570 660 716 720 729 731 741 747 ...
>  .. .. ..$ +: int [1:332302] 234 283 535 590 659 663 682 704 710 724 ...
>  .. ..$ chr3 :List of 2
>  .. .. ..$ -: int [1:212665] 46758 50637 50654 50691 50703 50723 50735
> 50789 54970 55050 ...
>  .. .. ..$ +: int [1:212274] 38885 50529 50545 50551 50581 50582 50583
> 50630 50695 54859 ...
>
>   ...            ...              ...
>
>  ..@ elementMetadata: NULL
>  ..@ elementType    : chr "ANY"
>  ..@ metadata       :List of 3
>  .. ..$ organism       : NULL
>  .. ..$ provider       : NULL
>  .. ..$ providerVersion: NULL
>
> ---- Original message ----
> >Date: Mon, 18 Oct 2010 19:48:37 -0700
> >From: Michael Lawrence <lawrence.michael@gene.com>
> >Subject: Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData
> >To: D.Strbenac@garvan.org.au
> >Cc: bioc-sig-sequencing@r-project.org
> >
> >   That coercion only works if the elements of your
> >   GenomeData are coercible to RangedData (which after
> >   coercion are combined into a single RangedData). So
> >   it would be good to know what's in your GenomeData.
> >   If each element is a list, as your error message
> >   suggests, it won't work, as there really is no way
> >   to convert a list to a RangedData.
> >
> >   Michael
> >
> >   On Mon, Oct 18, 2010 at 7:00 PM, Dario Strbenac
> >   <D.Strbenac@garvan.org.au> wrote:
> >
> >     Hello,
> >
> >     This conversion used to work before but it seems
> >     like it doesn't any longer.
> >
> >     > summary(rs)
> >        Length      Class       Mode
> >            25 GenomeData         S4
> >     > as(rs, "RangedData")
> >     Error in FUN(X[[1L]], ...) :
> >      no method or default for coercing "list" to
> >     "RangedData"
> >     > sessionInfo()
> >     R version 2.12.0 (2010-10-15)
> >     Platform: x86_64-pc-mingw32/x64 (64-bit)
> >
> >     locale:
> >     [1] LC_COLLATE=English_Australia.1252
> >      LC_CTYPE=English_Australia.1252
> >      LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> >     [5] LC_TIME=English_Australia.1252
> >
> >     attached base packages:
> >     [1] stats     graphics  grDevices utils
> >     datasets  methods   base
> >
> >     other attached packages:
> >     [1] BSgenome_1.18.0     Biostrings_2.18.0
> >     GenomicRanges_1.2.0 IRanges_1.8.0
> >
> >     loaded via a namespace (and not attached):
> >     [1] Biobase_2.8.0
> >
> >     _______________________________________________
> >     Bioc-sig-sequencing mailing list
> >     Bioc-sig-sequencing@r-project.org
> >     https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>

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